Biomarkers for Autism Spectrum Disorders

ABSTRACT

Methods of determining the risk of ASD in an individual are provided which comprise identifying the presence of one or more genomic mutations in one or more of the genes, PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1.

FIELD OF THE INVENTION

The present invention relates to genetic markers for Autism Spectrum Disorders (ASD).

BACKGROUND OF THE INVENTION

Autism is a heritable neurodevelopmental condition characterized by impairments in social communication and by a preference for repetitive activities. Autism is not a distinct categorical disorder but is the prototype of a group of conditions defined as Pervasive Developmental Disorders (PDDs) or Autism Spectrum Disorders (ASD), which include Asperger's Disorder, Childhood Disintegrative Disorder, Pervasive developmental disorder-not otherwise specified (PDD-NOS) and Rett Syndrome. ASD is diagnosed in families of all racial, ethnic and social-economic backgrounds with incidence roughly four times higher in males compared to females. Overall population prevalence of autism has increased in recent years to a current estimate of 20 in 10,000 with incidence as high as 60 in 10,000 for all autism spectrum disorders.

Data from several epidemiological twin and family studies provide substantial evidence that autism has a significant and complex genetic etiology. The concordance rate in monozygotic twins is 60-90% (Bailey 1995), and the recurrence rate in siblings of affected probands has been reported to be between 5-10% (Jones & Szatmari 1988) representing a 50 fold increase in risk compared to the general population. Although autism spectrum disorders are among the most heritable complex disorders, the genetic risk is clearly not conferred in simple Mendelian fashion.

In a minority of cases (˜10%), autism is part of a broader recognizable disorder (e.g. fragile X syndrome, tuberous sclerosis) or is associated with cytogenetically-detectable chromosome abnormalities. Moreover, co-morbidity of autism with microdeletion syndromes (e.g. William-Beuren and Sotos) and other genomic disorders (e.g. Prader-Willi/Angelman) suggests chromosomal imbalances are involved in the underlying etiology. The most frequent cytogenetic anomaly is an interstitial, maternally-inherited duplication of 15q11-13 (1-3%) encompassing the Prader Willi/Angelman Syndrome critical region. There are also a large number of cases with deletions in the q11.2 and q13.3 regions of chromosome 22. The 22q11.2 region is associated with velo-cardio-facial Syndrome and deletions at 22q13.3 appear to also represent a clinically definable syndrome. Both deletions are associated with the autistic phenotypes. Other chromosome loci associated with anomalies with a higher frequency of events observed in syndromic forms of ASD include 7q (see TCAG www.chr7.org), 2q37, 5p14-15, 17p11.2. In addition, reciprocal duplications overlapping the William-Beuren deletion region have been associated with the autism phenotype.

Genome-wide linkage scans have found evidence for susceptibility loci on almost all chromosomes with 7q yielding the most consistent results. Other loci with significant linkage include 2q (IMGSAC 2001), 3q and most recently 11p (AGP 10K study). In some instances, like 7q, there is considerable overlap between cytogenetic anomalies and linkage results. However, the lack of linkage found at 15q11-13 and 22q13.3 loci reflect considerable heterogeneity in ASD and suggest that these rearrangements are responsible for a particular ASD subtype involving genes that do not contribute to the phenotype in cytogenetically normal patients. Despite promising results, no specific genes within these linkage peaks have unequivocally been shown to contribute to autism.

Mutations associated with ASD have been reported in two neuroligin (NLGN3 and NLGN4) genes and more recently SHANKS; however, these account for only rare causes of ASD. Other genes have been implicated, but represent rare events or have not yet been validated by other studies.

Together these data suggest substantial genetic heterogeneity with the most likely cause of non-syndromic idiopathic ASD involving multiple epistatically-interacting loci.

The identification of large scale copy number variants (CNVs) represents a considerable source of genetic variation in the human genome that contributes to phenotypic variation and disease susceptibility found small inherited deletions in autistic kindreds suggesting possible susceptibility loci.

It would be desirable to identify genetic markers of ASD that facilitate in a determination of the risk of ASD in an individual, as well as to assist in the diagnosis of the condition.

SUMMARY OF THE INVENTION

A number of genetic markers have now been identified which are useful in assessing the risk of ASD in an individual, as well as being useful to diagnose the condition. The markers are useful both individually and in the form of a microarray to screen individuals for risk of ASD.

Thus, in one aspect of the present invention, a method of determining the risk of ASD in an individual is provided comprising:

-   -   probing a nucleic acid-containing sample obtained from the         individual for a gene encoding PTCHD1, wherein a determination         that the gene comprises a deletion of at least a portion of exon         1 is indicative of a risk of ASD in the individual.

In another aspect of the present invention, a method of determining the risk of ASD in an individual is provided comprising:

-   -   probing a nucleic acid-containing sample obtained from the         individual for a mutation that modulates the expression of at         least one gene selected from the group consisting of PTCHD1,         SHANK3, NFIA, DPP6, DPP10, GPR98, PQBP1, ZNF41 and FTSJ1,         wherein identification of a mutation that modulates the         expression of at least one of said genes is indicative of a risk         of ASD.

In another aspect of the invention, a method of determining the risk of ASD in an individual is provided comprising:

-   -   screening a biological sample obtained from the individual for         abnormal levels of at least one gene product expressed by a gene         selected from the group consisting of PTCHD1, SHANK3, NFIA,         DPP6, DPP10, GPR98, PQBP1, ZNF41 and FTSJ1, wherein a         determination that at least one of said gene products is         expressed at a level that varies from the level in a healthy         non-ASD individual is indicative of a risk of ASD.

In a further aspect of the invention, a method of determining the risk of ASD in an individual is provided comprising:

-   -   screening a nucleic acid-containing sample from the individual         for genomic sequence variations that modulate the expression of         PTCHD1.

These and other aspects of the present invention are described by reference to the following figures in which:

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow chart depicting the methodology used to identify ASD-specific CNVs;

FIG. 2 illustrates a genome-wide distribution of ASD-specific CNVs as described in Table 3;

FIG. 3 illustrates the chromosome 16p11.2 region as depicted in the Autism Chromosome Rearrangement Database;

FIG. 4 illustrates examples of CNVs observed in ASD families including probands having multiple de novo events (a); rearrangements in the SHANK3 gene (b); probands with chromosome X deletions (at PTCHD1) from female carriers (c) or inherited translocations in addition to an unrelated de novo deletion (d); overlapping events in unrelated probands either de novo (e) or inherited (f) at the DPP6 locus; and recurrent de novo events at chromosome 16p11.2 in unrelated probands either gains (h) or losses (g);

FIG. 5 illustrates examples of DPP6 and DPP10 ASD-related CNVs;

FIG. 6 illustrates examples of chromosome 22q11.2 and 16p11.2 ASD-related CNVs;

FIG. 7A illustrates the cDNA sequence of the PTCHD1 gene; and FIG. 7B illustrates the corresponding amino acid sequence; and

FIG. 8 illustrates ASD-related missense mutations identified in Table 7.

DETAILED DESCRIPTION OF THE INVENTION

A method of determining the risk of an autism spectrum disorder (ASD) in an individual is provided comprising screening a biological sample obtained from the individual for a mutation that may modulate the expression of at least one gene selected from the group consisting of PTCHD1, SHANK3, NFIA, DPP6, DPP10, DPYD, GPR98, PQBP1, ZNF41 and FTSJ1. Such genes are referred to herein as “ASD-associated” genes.

The term “an autism spectrum disorder” or “an ASD” is used herein to refer to at least one condition that results in developmental delay of an individual such as autism, Asperger's Disorder, Childhood Disintegrative Disorder, Pervasive Developmental Disorder-Not Otherwise Specified (PDD-NOS) and Rett Syndrome (APA DSM-IV 2000).

In the present method of determining ASD risk in an individual, a biological sample obtained from the individual is utilized. A suitable biological sample may include, for example, a nucleic acid-containing sample or a protein-containing sample. Examples of suitable biological samples include saliva, urine, semen, other bodily fluids or secretions, epithelial cells, cheek cells, hair and the like. Although such non-invasively obtained biological samples are preferred for use in the present method, one of skill in the art will appreciate that invasively-obtained biological samples, may also be used in the method, including for example, blood, serum, bone marrow, cerebrospinal fluid (CSF) and tissue biopsies such as tissue from the cerebellum, spinal cord, prostate, stomach, uterus, small intestine and mammary gland samples. Techniques for the invasive process of obtaining such samples are known to those of skill in the art. The present method may also be utilized in prenatal testing for the risk of ASD using an appropriate biological sample such as amniotic fluid and chorionic villus.

In one aspect, the biological sample is screened for nucleic acid encoding selected genes in order to detect mutations associated with an ASD. It may be necessary, or preferable, to extract the nucleic acid from the biological sample prior to screening the sample. Methods of nucleic acid extraction are well-known to those of skill in the art and include chemical extraction techniques utilizing phenol-chloroform (Sambrook et al., 1989), guanidine-containing solutions, or CTAB-containing buffers. As well, as a matter of convenience, commercial DNA extraction kits are also widely available from laboratory reagent supply companies, including for example, the QIAamp DNA Blood Minikit available from QIAGEN (Chatsworth, Calif.), or the Extract-N-Amp blood kit available from Sigma (St. Louis, Mo.).

Once an appropriate nucleic acid sample is obtained, it is subjected to well-established methods of screening, such as those described in the specific examples that follow, to detect genetic mutations indicative of ASD, i.e. ASD-linked mutations. Mutations, such as genomic copy number variations (CNVs), which include gains and deletions of segments of DNA, for example, segments of DNA greater than about 1 kb, such as DNA segments between about 300 and 500 kb, as well as base pair mutations such as nonsense, missense and splice site mutations, including sequence mutations in both coding and regulatory regions of a gene, have been found to be indicative of ASD.

ASD-linked mutations such as CNVs are not restricted to a single chromosome, but rather have been detected on a multiple chromosomes such as the X chromosome, chromosome 15 and chromosome 21, and on various regions of the same chromosome such as at Xp11 and Xp22. Examples of CNVs that have been determined to be linked to ASD include a deletion on chromosome Xp22 including at least a portion of exon 1 of the PTCHD1 gene; a duplication on chromosome 15q11; and a deletion within the SHANK3 gene.

Genomic sequence variations of various types in different genes have been identified as indicative of ASD. CNVs in the DPP10 gene, including intronic gains, such as a 105 kb intronic gain, and exonic losses, such as a 478 kb exonic loss, both of which are more specifically identified in Table 1, have been identified; CNVs in the DPP6 gene, such as a 66 kb loss encompassing exons 2 and 3 and gains such as a CNV encompassing the entire DPP6 gene, a 270 kb exonic gain (exon 1), and a 16 kb intronic gain (see Table 1); CNVs in the SHANK3 gene such as a 276 kb loss; and CNVs in the DYPD gene such as a loss of the entire gene.

In one embodiment, genomic sequence variations that inhibit the expression of PTCHD1 have been linked to ASD. The terminology “inhibit expression” refers broadly to sequence variations that may inhibit, or at least reduce, any one of transcription and/or translation, as well as the activity of the PTCHD1 protein. For example, a CNV in the PTCHD1 gene comprising a large deletion of the coding region which results in at least a reduction of the expression of PTCHD1 protein has been found to be indicative of ASD. Although the CNV is not particularly restricted, the CNV deletion may include, for example, at least a portion of exon 1, but may additionally include surrounding regions as well, such as intron 1, in whole or in part, or a portion or more of the upstream region thereof.

Genomic sequence variations other than CNVs have also been found to be indicative of ASD, including, for example, missense mutations which result in amino acid changes in a protein that may also affect protein expression. In one embodiment, missense mutations in the PTCHD1 gene have been identified which are indicative of ASD, including missense mutations resulting in the following amino acid substitutions in the Ptchd1 protein: L73F, I173V, V195I, ML336-337II and E479G.

To determine risk of ASD in an individual, it may be advantageous to screen for multiple genomic mutations, including CNVs and other mutations as indicated above applying array technology. In this regard, genomic sequencing and profiling, using well-established techniques as exemplified herein in the specific examples, may be conducted for an individual to be assessed with respect to ASD risk/diagnosis using a suitable biological sample obtained from the individual. Identification of one or more mutations associated with ASD would be indicative of a risk of ASD, or may be indicative of a diagnosis of ASD. This analysis may be conducted in combination with an evaluation of other characteristics of the individual being assessed, including for example, phenotypic characteristics.

In view of the determination of gene mutations which are linked to ASD, a method for determining risk of ASD in an individual is also provided in which the expression or activity of a product of an ASD-linked gene mutation is determined in a biological protein-containing sample obtained from the individual. Abnormal levels of the gene product or abnormal levels of the activity thereof, i.e. reduced or elevated levels, in comparison with levels that exist in healthy non-ASD individuals, are indicative of a risk of ASD, or may be indicative of ASD. Thus, a determination of the level and/or activity of the gene products of one or more of PTCHD1, SHANK3, NFIA, DPP6, DPP10, DYPD, GPR98, PQBP1, ZNF41 and FTSJ1, may be used to determine the risk of ASD in an individual, or to diagnose ASD. As one of skill in the art will appreciate, standard assays may be used to identify and quantify the presence and/or activity of a selected gene product.

Embodiments of the invention are described by reference to the following specific examples which is not to be construed as limiting.

EXAMPLE 1 DNA Samples and Population Structure

The study included 426 ASD families All of the index cases met Autism Diagnostic Interview-Revised (ADI-R) and Autism Diagnostic Observation Schedule (ADOS) criteria or on a clinical best estimate (Risi et al. J Am Acad Child Adolesc Psychiatry 2006; 45(9):1094-103). Thirty-two of these carried a cytogenetic chromosome rearrangement; 18 were detected by karyotyping 328 of 412 samples that originated from child diagnostic centres at the Hospital for Sick Children in Toronto and from St. John's, Newfoundland; 14 were already known to carry karyotypic anomalies (see Table 1 for information on these 32 patients). Affected and unaffected siblings were also assessed, and 56% (237/426) had one child (simplex) and 44% (189/426) had more than one child (multiplex) with ASD. Most cases were screened for fragile X mutations (75%) and if detected they were not included in the study. Most experiments were performed on blood genomic DNA (80%), otherwise the source was cell lines, e.g. lymphoblast cell lines. Population ancestry was estimated using STRUCTURE (Falush et al. Genetics 2003; 164(4):1567-87; Pritchard et al. Genetics 2000; 155(2):945-59).

TABLE 1 Cytogenetic Analysis Sample Phenotype/Family Breakpoint CNV Analysis ID type Karyotype Location RefSeq Genes Chr 1 NA0008- Simplex family 46, XX, t (2;6) 2q33.1: SATB2 2p11.2 000 ASD, developmental (q32;p22) 200,096,682- (50863L) dyspraxia unknown 200,154,790 6p22.3: No known 6p21.33 21,561,566- genes 11p13 21,644,040 13q21.33 14q11.2 14q32.33 2 NA0005- Simplex family 46, XX, t (4;5) 4q21.3 Several 1p13.2 000 ASD, seizure (q21;q13) 2q37.3 (53601L) disorder, obesity, unknown 3q29 macrocephaly 5q14.2-q14.3: Several 5q15 82,802,678- 5q21.3 91,285,973 8p23.1 14q11.2 14q11.2 15q11.2 3 NA0039- Simplex family 46, XX, der (22) See CNV See CNV 9q32 000 ASD, submucous t (14;22) (q32; q13) 14q32.33 (69736) deft, globally pat inherited 15q13.3 developmentally 22q13.31- delayed, large ears, q31.33 short forehead, distally tapere fingers, severe pes planovalgus 4 SK0283- Simplex family 47, XX, ring See CNV See CNV 1p22.3 003 ASD chromosome 1 1q21.2- (72309) de novo q21.3 3p26.1 4p13 4q33 5q31.3 6p12.3 7p14.1 7q34 14q11.2 15q11.2 17q21.31 5 SK0044- Simplex family 46, XY, t (1;2) 1p31.1 : NEGR1 7p14.1 003 ASD (p22.1;p23) pat 72,065,578- (50067) der (13;15) 72,163,007 (q10;q10) mat 2p24.3 : No known inherited 12,376,807 genes 12,733,637 13q10: in progress 15q10: in progress 6 SK0182- Simplex family 46 XY, t (1;9) 1q24.2: No known 2p24.3 003 ASD (q25;p13) 167,452,268- genes (52065) inherited 167,522,136 9p12: No known 14q11.2 45,695,701- genes 45,737,008 7 SK0335- Simplex Family 46, XX, t (2;10) 2q23.1: LOC401431, 2p13.3 003 ASD, mental (q22;q22.3) 148,938,284- ATP6VOE2 (72815) retardation unknown 149,125,547 10q23.31: SLC16Al2, 3q29 91,265,490- PANK1, 5p13.1 91,461,660 MPHOSPH1 6p21.32 8p23.1 9q32 14q11.2 15q11.2 16p11.2- 11.1 17q21.31 20p12.1 8 SK0126- Multiplex family 46, XY, t (2;11) 2p11.2: No known 2q34 003 ASD (p11.2;q13.3) pat 89,117,655- genes (59144) inherited 89,158,494 11q13.1: POLA2, 64,821,333- CDC42EP2, 64,861,285 DPF2 9 SK0152- Multiplex family 46, XY, inv 3p24: not 3p25.1- 003 ASD, oral motor (3) (p24;q24), available p24.3 (41548L) apraxia, poor balance t (5;7) (p15p13) 3q24: not 3p12.3 and coordination, de novo available mild hypotonia, walks 5p14.3: CDH18 5p15.31- with a wide gait, 19,825,926- p15.2 severe language 19,883,410 delay, moderate 7p13: No known 6q16.1 intellectual disability, 46,618,434- genes 7p14.1 some facial features 46,733,542 10q11.22 of Cri du Chat 12p11.21 12q12 14q11.2 14q32.33 15q11.2 16q21 17q21.31 18q12.2 10 SK0105- Multiplex family 46, XY, inv (4) 4p15.3: No known 10q11.21 003 ASD, primarily non- (p12;p15.3) mat 12,173,445- genes (27155L) verbal, profound inherited 12,335,572 developmental delay 4p12: GABRG1 13q14.2 44,876,353 (breakpoint 16q21 46,024,486 region is located 17q21.31 in inton 7) 11 SK0205- Simplex family 46, XX, del See CNV See CNV 3q29 004 ASD (5) (p15.1) 5p15.33- (56242) de novo p15.2 5q15 10q11.22 10q21.3 10q26.3 14q11.2 15q11.2 17q21.31 17q21.31 22q11.21 12 SK0061- Simplex family 46, XV, t (5;7) 7q31.31: No known No CNV detected 003 ASD, developmental (q15;q31.32) 118,928,065- genes (44951) delay unknown 119,006,076 5q14.3: No known 88,849,193- genes 88,891,151 13 SK0195- Simplex family 46, XY, t (5;8;17) 5q31.1: KLHL3 2p16.1 003 ASD (q31.1;q24.1;q21.3) 136,979,583- (55310) de novo 137,038,092 8q24.22: No known 10q23.1 132,448,049- genes 132,512,973 17q21.31: LRRC37A2, 14q11.2 41,893,216- ARL17P1, 17q21.31 42,093,636 LOC641522, NSF 14 SK0133- Simplex family 46, XY, t (6;7) 6p12.1: DST, c6orf65 2q37.1 003 ASD (p11.2;q22) 56,805,919- (46012) pat inherited 56,967,398 7q22.1: No known 5q14.3 97,933,646- genes 7q33 97,973,368 8q23.2 9p21.3 11q25 12q21.33 13q21.32 15 SK0043- Multiplex family 46, XY, t (6;9) 6q11.2-q12: No known 8p23.2 003 ASD (q10;q12) 63,464,452- genes (29346) unknown 63,511,410 9q21.11: PIPSK1B 15q11.2 68,599,032- 68,682,365 16 SK0181- Simplex family 46, XY, t (6;14) 6q12: No known 3p14.1- 004 ASD (q13;q21) 69,241,818- genes p13 (52191) de novo 69,279,457 14q21.1-q21.2: LRFN5, cl4orf155, 4q28.3 40,807,716- c14orf28, BTBD5, 44,806,460 KIAA0423, PRPF39, FKBP3, AK093422, KIAA1596, FANCM, c14orf106 17 SK0083- Simplex family 46, XY, del (7) 7q31.1: IMMP2L, LRRN3, 1q31.1 003 ASD, (q31.1q31.32) 108,272,363- DOCK4, ZNF277P, (50800L) craniosynostosis, de novo 108,337,904 IFRD1... to ... developmental verbal 7q31.31: ASZ1, CFTR, 2p23.3 dyspraxia, motor 119,007,999- CTTNBP2, LSM8, 4q35.2 delay 119,335,246 ANKRD7 6p24.2 7q31.1- q31.31 7q36.2 8q24.21 10p11.23 14q11.2 17q21.31 18 SK0131- Simplex family 46, XX, del (7) 7q31.1: FOXP2, MDFIC, 2p22.2 003 Autistic features, (q31.2q32.2) 113,181,975- TFEC, TES, 3p21.31 (39989) speech-language (D7S486-, D7S522-) 113,518,235 CAV2, CAV1 disorder de novo, 7q32.2: ...to...IRF5, 4q31.21 (developmental WBS inv-2 128,540,690- TNPO3, TSPAN33, 7p14.1 verbal dyspraxia), de novo 128,796,716 SMO, FAM40B, 7q31.1- dysmorphic features, KIAA0828 q32.2 mild developmental 8q13.3 delay, unable to 10q11.22 cough/sneeze/laugh 10q26.2 spontaneously 13q21.33 14q11.2 14q11.2 15q11.2 17q12 22q11.22 19 SK0002- Simplex family 46, XX, inv (7) 7p21.1: No known 4q28.3 003 ASD, psychosis (p15.3;q22.1) 18,284,397- genes (50002) unknown 18,302,387 7q22.3: SPRK2 5p15.1- 104,360,659- 15.2 104,549,945 15q11.2 20 SK0211- Simplex family 46, XX, inv (7) 7q21.3: No known 7q22.1 003 ASD, mild elevation (q22q34) mat 96,943,657- genes (58892) of lactate inherited 96,985,663 7q34: TAS2R4, 9p21.1 140,920,721- TAS2R5 104,958,207 21 SK0040- Multiplex family 46, XY, t (7;8) 7p15.3: No known 2q37.3 003 ASD, ADHD, severe (p15;q22), t 21,825,126- genes (55449) anxiety attacks, (10;11)(q26;q23) 21,869,196 seizures, difficulties unknown 8q22.2: STK3 10q21.3 with fine and gross 99,652,299- 11q22.3 motor skills 99,823,618 10q26: Multiple genes 14q11.2 127,985,179- 14q11.2 131,365,091 11q23: Multiple genes 15q11.2 109,979,883- 22q11.22 111,597,476 22q11.23 22 SK0145- Simplex family 46, XX, t (7;11) 7q31.2: No known 1p36.11 003 ASD (q31;q25) mat 114,573,150- genes 2p24.2 (67955) inherited 114,611,613 11q25: No known 3p23 133,882,647- genes 5p15.33 134,001,155 6p22.2 7p14.1 8q13.3 10p12.1 12p12.3 14q11.2 15q23- 24.1 19q13.43 23 SK0031- Simplex family 46, XV, t (7;13) 7q31.2: ST7 5p13.2 003 ASD, very little (q31.3;q21) mat 116,270,156- 6p22.1- (68160L) language, global inherited 116,458,896 21.33 developmental delays 13q21.1: No known 9p23 54,559,087- genes 14q32.2 54,739,454 15q11.2 17q21.31 22q11.23 24 SK0073- Simplex family 47, XX, idic 15q13: LOC400968, 1q25.2 003 ASD, developmental (15)q13) 28,918,525- LOC283755, 2p23.3 (57283L) delay, delayed de novo 31,848,963 POTE15, OR4M2, 4p16.3 expressive and OR4N4...to... 4q35.1 receptive language ARHGAP11A, 5q31.1 c15orf45, 9p21.1 GREM1, 14q11.2 RYR3 15q11.2- 13.3 16p11.2 16p11.2 25 SK0218- Multiplex family 46, XX, del 18q21.32: See CNV 12p13.33 003 ASD, cleft palate, (18) (q21) 55,690,398- 15q11.2 (60340) club feet, mild-facial de novo 55,884,029 17q21.31 hypoplasia, heart 18q21.32- defect q23 19q13.42 20p11.23 26 SK0215- Simplex family 46, XY, t (19,21) 19p13.2: EVI5L, FLJ22184, 1p21.3 006 ASD (p13.2;q22.12) 7,804,294- LRRC8E, MAP2K7, (58449) inherited 7,896,711 SNAPC2, CTXN1 21q22.12: No known 17p11.1- 36,091,999- genes p11.2 36,191,098 27 SK0136- Simplex family 46, X, der (Y) Not 4p13 003 ASD t (Y;15) (q12;p11.2) available 8p23.2 (51253) pat inherited 8q24.23 10p12.1 15q11.2 15q26.3 28 SK0243- Simplex Family 46, XY, del (15) See CNV See CNV 1q21.1 003 ASD (q23q24.2) 2p22.2 (67941) de novo 3q27.3 7p22.3 7p14.1 10p13 11p15.1 15q23- q24.2 17q12 17q21.31 29 SK0245- Simplex Family 46, XY, trp (15) See CNV See CNV 6q14.1 005 ASD, epicanthal (q11.2q13) 7p14.1 (68517) folds, drooping eyes de novo 10p13 11p15.1 14q11.2 14q32.33 15q11.2- q13.3 19p13.2 30 NA0097- Simplex Family 46, XX, t (11;12) 11q23: 2p25.3- 000 ASD (q23.3;p13.3) not 2p15 (82361L) unknown available 3p24.2 12p11.21 12p13.32- Multiple genes 14q11.2 p13.31: Xp22.33- 4,341,718- Xp22.31 7,918,138 31 SK0300- Multiplex Family 46, X, inv (Y) Not 4p16.1 003 ASD, NF1 (p11.2q11.2) pat available 5p15.33 (77447) inherited 6p25.1 8q24.23 11p15.4 14q11.2 15q11.2 15q21.2 Xp11.23 32 SK0094- Multiplex Family 46, XX, ins (21;?) Not 7q21.2 005 ASD (p11.2;7) available 9q32 (49304) unknown 10q11.22 14q32.33 Xq23 CNV Analysis CNV Size (bp) Location AS/Str^(a) RefSeq Genes Comments  1 Loss 917,200  89,056,400- No/NS No known NFLD  89,973,600  genes Gain 54,600  30,134,300- Yes/NS ZNRD1,  30,188,900  PPP1R11, RNF39, TR1M31 Gain 54,200  35,332,700- No/NS SLC1A2  35,386,900  Loss 28,200  69,642,500- No/NS No known  69,670,700  genes Gain 549,300  21,490,300- No/NS No known  22,039,600  genes Loss 64,000 106,152,000- No/NS No known 106,216,000  genes  2 Gain 128,963 112,783,876- Yes/NS ST7L, NFLD 112,912,839  CAPZA1 Loss 602,914 242,127,468- No/S 10 genes Error! 242,730,382  Hyperlink reference not valid. Loss 43,033 196,922,636- No/NS MUC20, 196,965,669  MUC4 Loss 48,627  97,076,449- No/NS No known  97,125,076  genes Loss 13,000 109,391,000- Yes/NS No known 109,404,000  genes Gain 448,146  12,039,387- No/S FAM86B1,  12,487,533  DEFB130, LOC440053 Gain 223,579  19,272,965- No/S 6 OR genes  19,496,544  Gain 650,430  21,407,981- No/S No known  22,058,411  genes Gain 1,642,961  18,446,422- No/NS LOC283755, Error!  20,089,383  POTE15, Hyperlink OR4M2, reference OR4N4 not valid.  3 Gain 498,000 114,038,000- No/NS 7 genes NFLD 114,536,000  Unaffected sibling Gain 1,436,000 104,920,000- No/NS 6 genes with ADHD has 106,356,000  46, XX, der (14) Gain 502,500  29,796,300- No/NS CHRNA 7 t (14; 22)  30,298,800  (q32; q13) Loss 3,231,700  46,277,400- Yes/NS 40 genes +  49,509,100  SHANK3  4 Gain 23,993  87,417,351- Yes/NS No known SK  87,441,344  genes Gain 1,451,926 148,095,537- Yes/S 36 genes 149,547,463  Loss 44,458  5,365,506- Yes/S No known  5,409,964  genes Gain 95,508  44,762,996- Yes/S No known  44,858,504  genes Loss 82,224 171,715,627- Yes/NS No known 171,797,851  genes Loss 355,649 140,658,658- Yes/NS 6 genes 141,014,307  Gain 13,950  46,962,122- No/NS GPR116  46,976,072  Loss 102,939  38,041,635- No/NS STARD3NL,  38,144,574  TARP Loss 169,191 141,813,948- No/NS PRSS1 141,983,139  Loss 583,148  21,455,546- No/S No known  22,038,694  genes Loss 1,632,769  18,427,103- No/S LOC283755,  20,059,872  POTE15, OR4M2, OR4N4 Loss 140,746  41,570,665- No/NS KIAA1267  41,711,411   5 Gain 85,900  39,828,000- No/NS CDC2L5 SK  39,913,900   6 Gain 15,100  14,304,500- No/NS No known SK  14,319,600  genes Younger brother Gain 288,100  19,204,300- No/S 6 genes has the same  19,492,400  translocation and severe speech and language disorder but does not meet ASD criteria on ADOS.  7 Gain 374,900  70,152,900- Yes/NS 6 genes Others  70,527,800  Non-Canadian Gain 43,033 196,922,636- No/NS MUC20, family 196,965,669  MUC4 Loss 272,618  38,534,384- Yes/S LIFR  38,807,002  Gain 162,900  32,344,099- Yes/NS C6orf10,  32,506,999  BTNL2 Gain 21,783  12,264,620- No/NS No known  12,286,403  genes Gain 22,000 114,153,000- No/S ORM1, 114,175,000  ORM2 Gain 331,503  21,717,112- No/S No known  22,048,615  genes Gain 1,516,085  18,427,100- No/S LOC283755,  19,943,185  POTE15, OR4M2, OR4N4 Gain 266,336  34,325,041- No/NS No known  34,591,377  genes Gain 201,731  41,518,102- No/S KIAA1267  41,719,833  Loss 27,500  14,973,800- Yes/S C200rf133  15,001,300   8 Loss 3,000 213,013,000- Yes/NS ERBB4 Other 213,016,000  Canadian Family  9 Loss 1,409,600  15,125,800- Yes/S 12 genes Other  16,535,400  Canadian Gain 55,000  78,902,000- Yes/S ROBO1 Family  78,957,000  Previously Loss 3,429,389  9,275,811- Yes/S 8 genes described in a  12,705,200  manuscript by Loss 60,058  95,556,287- No/S No known Harvard et al¹.  95,616,345  genes The 3p25.1, Gain 35,243  38,096,725- No/NS No known 5p15.31-p15.2  38,131,968  genes and 18q12.2 Gain 455,130  47,030,119- No/S ANXA8 deletions were  47,485,249  identified in Gain 63,728  31,904,362- No/S No known Harvard, C. et al  31,968,090  genes using BAC CGH. Loss 422,842  40,584,198- Yes/S YAF2, The deletion size  41,007,040  ZCRB1 has been refined Gain 491,397  21,584,229- No/S No known here using SNPs.  22,075,626  genes Older sibling also Gain 22,269 106,223,861- No/NS No known has ASD but has 106,246,130  genes a normal 46, XX Loss 1,632,718  18,446,422- No/S LOC283755, karyotype  20,079,140  POTE15, Maternal OR4M2, aunt with OR4N4 schizophrenia Loss 91,432  63,768,909- Yes/NS No known and a  63,860,341  genes maternal uncle Gain 219,797  41,500,036- No/NS KIAA1267 with Down  41,719,833  syndrome Loss 816,914  32,174,061- Yes/S KIAA1328,  32,990,975  c18orf10, FHOD3 10 Gain 1,098,400  41,956,500- Yes/NS RET, SK  43,054,900  RASGEF1A, Described BMS1L, previously in ZNF11B, Vincent et al.² MGC16291, Affected brother, GALNACT-2 apparently Gain 162,300  47,414,800- Yes/NS MED4, unaffected mother  47,577,100  NUDT15, and unaffected SUCL42 maternal Loss 56,600  61,854,900- Yes/NS No known grandfather all  61,911,500  genes have the same Gain 238,600  41,521,600- No/NS KIAA1267 inversion. Distal  41,760,200  4p15.3 breakpoint maps ~12 Mb to a region previously indicated to show linkage to autism. 11 Gain 96,068 199,226,000- No/NS LMLN, SK 199,322,068  LOC348840 FISH analysis with Loss 13,800,984    81,949- Yes/S >50 genes subtelomeric  13,882,933  probe (containing Loss 70,891  97,054,185- No/NS No known D552488) was  97,125,076  genes consistent with a Gain 1,121,866  46,363,383- No/S SYT15, ANXA8, terminal deletion  47,485,249  ANXA8L1, on 5p. PPYR1, GPRIN2 Loss 29,732  67,747,770- No/NS CTNNA3  67,777,502  Gain 244,432 135,079,000- No/S SYCE1; CYP2E1 135,323,432  Gain 217,035  19,272,965- No/S OR4K1, OR4N2,  19,490,000  OR4K5, OR4K2 Gain 1,662,300  18,427,100- No/S LOC283755,  20,089,400  POTE15, OR4M2, OR4N4 Gain 65,845  41,006,823- No/S No known  41,072,668  genes Gain 187,028  41,521,621- No/NS KIAA1267  41,708,649  Gain 150,753  17,265,500- No/S DGCR6, PRODH,  17,416,253  DGCR2 12 No CNV detected Other Non-Canadian Family 13 Gain 47,900  57,314,000- No/NS No known Other  57,361,900  genes Canadian Loss 17,500  83,772,000- Yes/NS NRG Family  83,789,500  Gain 288,100  19,204,300- No/NS OR4K1, OR4N2,  19,492,400  OR4M1, OR4K5, Gain 644,700  41,521,600- OR4Q3, OR4K2  42,166,300  No/S KIAA1267 14 Gain 314,000 232,076,000- Yes/NS MGC43122, Other 232,390,000  NMUR1, Canadian MGC35154, NCL Family B3GN77 CNV seen at Gain 633,400  89,492,800- Yes/NS CETN3, 11q25 is in the  90,126,200  LOC153364, same breakpoint POLR3G, region as Sample MASS1 SK0145-003 Loss 3,000 136,255,000- No/NS No known 136,258,000  genes Loss 32,000 111,182,000- No/NS No known 111,214,000  genes Loss 8,200  25,073,900- Yes/NS No known  25,082,100  genes Gain 369,000 133,855,000- No/S No known 134,224,000  genes Gain 19,700  90,807,700- Yes/NS No known  90,827,400  genes Loss 2,500  65,576,300- Yes/NS No known  65,578,800  genes 15 Loss 35,040  3,984,190- No/NS CSMD1 SK  4,019,230  Sibling also Gain 1,713,200  18,376,200- No/S LOC283755, has ASD  20,089,400  POTE15, but a normal OR4M2, OR4N4 46, XY karyotype 16 Loss 5,346,900  65,286,300- Yes/S 13 genes SK  70,633,200  Loss 254,000 135,282,000- No/NS No known 135,536,000  genes 17 Loss 15,000 186,702,000- No/S No known Other 186,717,000  genes Canadian Gain 26,300  25,138,000- Yes/NS No known Family  25,164,300  genes Described Gain 21,314 188,232,000- Yes/S No known previously 188,253,314  genes in Feuk Gain 188,500  11,479,600- Yes/NS No known et a1.³  11,668,100  genes Loss 11,023,506 108,200,381- Yes/S >50 genes 119,223,887  Loss 26,297 152,027,450- Yes/NS No known 152,053,747  genes Gain 48,000 127,951,000- Yes/NS No known 127,999,000  genes Gain 26,700  30,893,400- Yes/NS No known  30,920,100  genes Loss 219,458  19,272,965- No/S OR4K1, OR4N2,  19,492,423  OR4M1, OR4K5, OR4Q3, OR4K2 Loss 117,521  40,897,617- No/NS PLEKHM1  41,015,138  18 Gain 67,740  37,848,232- No/NS No known Other  37,915,972  genes Canadian Gain 52,599 147,754,068- Yes/NS CCR5, CCRL2, Family 147,806,667  CCR2 Described Gain 120,171 145,146,000- No/S GYPE previously 145,266,171  in Feuk Gain 147,076  38,096,725- No/NS AMPH et a1.³  38,243,801  Loss 15,486,721 113,335,000- Yes/S >50 genes 128,821,721  Gain 261,985  72,881,221- Yes/NS MSC,  73,143,206  TRPA1 Gain 455,100  47,030,100- No/NS ANXA8  47,485,200  Gain 91,077 128,501,014- Yes/S DOCK1 128,592,091  Loss 44,235  69,634,065- No/NS No known  69,678,300  genes Loss 222,786  19,272,965- No/NS OR4K1, OR4N2,  19,495,751  OR4M1, OR4K5, OR4Q3, OR4K2 Gain 637,249  21,462,466- No/S No known  22,099,715  genes Gain 1,662,280  18,427,103- No/NS LOC283755,  20,089,383  POTE15, OR4M2, OR4N4 Gain 29,984  31,471,515- No/NS No known  31,501,499  genes Gain 810,876  20,772,047- No/NS 6 genes  21,582,923  19 Gain 765,000 132,195,000- No/S No known Other 132,960,000  genes Non Gain 239,100  14,940,400- No/S No known Canadian-  15,179,500  genes Family Gain 1,713,200  18,376,200- Yes/S LOC283755,  20,089,400  POTE15, OR4M2, OR4N4 20 Gain 379,000 100,393,000- No/NS 10 genes Other 100,772,000  Non Canadian Loss 135,100  30,408,400- No/NS No known Family  30,543,500  genes Mother and unaffected twin sister have the same karyotype; 7q34 breakpoint overlaps with a ASD translocation patient 21 Loss 95,959 242,634,423- No/S No known Other 242,730,382  genes Non- Loss 144,903  67,734,600- No/S CTNNA3 Canadian  67,879,503  Family Loss 62,995 104,729,456- No/NS No known Unaffected sister 104,792,451  genes with normal Gain 219,458  19,272,965- No/NS OR4K2, OR4N2, female karyotype,  19,492,423  OR4K1, OR4K5 has difficulties in Gain 224,329  21,784,072- No/NS No known some muscles,  22,008,401  genes difficulties with Gain 1,662,280  18,427,103- No/S LOC283755, fine and gross  20,089,383  POTE15, motor skills, OR4M2, OR4N4 severe anxiety Loss 515,645  21,031,117- No/NS PRAME, attacks, not able  21,546,762  SUHW2, to relate to peers SUHW1, and is affected by GGTL4 noise Gain 269,129  23,975,202- No/S CTA, LRP5L  24,244,331  22 Gain 192,600  26,231,500- Yes/NS 8 genes Other  26,424,100  Canadian Gain 14,233  17,416,366- Yes/NS No known Family  17,430,599  genes Apparently Gain 28,509  34,844,620- Yes/NS No known unaffected  34,873,129  genes mother Gain 3,029,476    165,712- Yes/NS 28 genes has the same  3,195,188  7q31.2 and Gain 25,841  25,576,804- Yes/NS LRRC16 11q25  25,602,645  breakpoints Gain 20,412  37,494,999- No/NS No known  37,515,411  genes Gain 28,933  72,911,162- Yes/NS MSC  72,940,095  Loss 98,961  27,642,965- No/S PTCHD3  27,741,926  Gain 37,831  18,855,833- No/NS No known  18,893,664  genes Gain 464,929  21,551,291- No/NS No known  22,016,220  genes Gain 435,603  70,053,228- Yes/NS 9 genes  70,488,831  Gain 308,600  63,476,500- Yes/NS 18 genes  63,785,100  23 Loss 3,000  36,495,800- Yes/NS No known Other  36,498,800  genes Non Gain 79,600  29,967,200- No/NS HLA-A Canadian  30,046,800  Family Loss 112,800  11,895,600- No/NS No known  12,008,400  genes Gain 772,400  99,015,100- Yes/S 8 genes  99,787,500  Gain 1,378,000  18,711,400- No/S LOC283755,  20,089,400  POTE15, OR4M2, OR4N4 Gain 597,300  41,569,000- No/NS 6 genes  42,166,300  Gain 251,200  23,989,000- No/S CTA-246H3.1,  24,240,200  LRP5L 24 Gain 424,000 176,522,000- Yes/NS 6 genes SK 176,946,000  Described Gain 703,500  24,701,300- Yes/NS 7 genes previously in  25,404,800  Kwasnicka- Gain 997,460  1,692,240- Yes/NS 12 genes Crawford et al.⁴  2,689,700  Gain 311,000 185,856,000- Yes/NS CASP3, 186,167,000  CCDC111, MLF1IP, ACSL1 Gain 93,000 134,426,000- Yes/S No known 134,519,000  genes Loss 362,900  30,452,800- Yes/NS No known  30,815,700  genes Gain 414,900  21,660,700- No/NS No known  22,075,600  genes Gain 11,922,600  18,376,200- Yes/S >50 genes  30,298,800  Gain 1,543,900  28,062,200- No/NS >20 genes  29,606,100  Gain 658,600  30,589,900- No/NS >20 genes  31,248,500  25 Loss 92,328  1,760,084- Yes/S CACNA2D4, SK  1,852,412  ADIPOR2, As noted in LRTM2 the Autism Loss 1,613,450  18,446,422- No/S LOC283755, Chromosome  20,059,872  POTE15, Rearrangment OR4M2, Database there OR4N4 are 5 addition Gain 190,234  41,518,415- No/NS KIAA1267 reported cases of  41,708,649  abnormalities Loss 20,358,999  55,756,601- Yes/S >50 genes involving 18q;  76,115,600  Sibling has a Loss 68,786  59,971,717- No/NS KIR3DP1, normal 46, XY  60,040,503  KIR2DL1, karyotype also is KIR3DL1, affected with KIR2DL4, autism and has KIR2DS4 oromotor Gain 128,457  19,740,012- Yes/NS RIN2 difficulties.  19,868,469  26 Loss 1,092,500  97,271,600- Yes/S FLJ35409, Other  98,364,100  DPYD Canadian Family Gain 503,100  21,634,900- Yes/NS FAM27L Patient has an  22,138,000  unaffected sister with the same karyotype 27 Gain 42,400  44,809,500- No/NS No known SK  44,851,900  genes Gain 234,580  2,335,310- No/NS No known  2,569,890  genes Loss 138,000 137,757,000- No/NS No known 137,895,000  genes Loss 51,400  27,690,500- No/NS PTCHD3  27,741,900  Loss 558,300  18,676,700- No/NS LOC283755  19,235,000  Gain 388,100  99,827,900- No/NS PCSK6, TARSL2, 100,216,000  TM2D3, OR4F6 28 Loss 333,539 145,700,996- No/NS No known SK 146,034,535  genes Gain 52,951  37,847,789- No/NS No known  37,900,740  genes Gain 91,422 187,897,578- No/S KNG1, 187,989,000  EIF4A2 Gain 29,778    141,322- No/NS No known    171,100  genes Loss 32,636  38,092,579- No/NS No known  38,125,215  genes Loss 1,570  13,096,593- No/NS No known  13,098,163  genes Gain 21,766  18,905,796- No/NS MRGPRX1  18,927,562  Loss 4,289,500  69,601,300- Yes/S 55 genes  73,890,800  Gain 38,247  31,463,252- No/NS No known  31,501,499  genes Gain 83,359  41,636,474- No/NS No known  41,719,833  genes 29 Loss 47,288  79,036,117- No/NS No known SK  79,083,405  genes Loss 57,861  38,067,354- No/NS No known  38,125,215  genes Loss 2,538  13,095,625- No/NS TARP  13,098,163  Loss 12,459  18,905,796- No/NS MRGPRX1  18,918,255  Loss 219,458  19,272,965- No/S 6 genes  19,492,423  Gain 27,408 106,223,861 No/NS No known 106,251,269 genes Gain 11,871,747  18,427,100 Yes/S >50 genes  30,298,847 Loss 132,251  6,902,567 No/S EMR4,  7,034,818 FLG25758, MBD3L2, ZF557 30 Gain 63,451,406^(b)    2,994 Yes/S >50 genes NFLD  63,454,400  Loss 159,273  25,980,400- No/NS No known  26,139,673  genes Gain 236,006  31,065,545- No/S DDX11,  31,301,551  OVOS2 Gain 489,269 21,498,204 No/NS No known 21,987,473 genes Loss 5,825,311     34,419- Yes/S 21 genes  5,859,730  31 Gain 35,832  7,801,488- Yes/NS SORCS2 SK  7,837,320  Gain 124,630    752,190- No/S ZDHHC11    876,820  Loss 215,567  4,200,904- Yes/S No known  4,416,471  genes Loss 198,193 137,757,137- No/S No known 137,955,330  genes Loss 54,390  6,845,440- Yes/S OR10A2,  6,899,830  OR1044, OR2D2, OR2D3 Loss 229,676  19,272,965- No/NS 6 genes  19,502,641  Loss 1,908,356  18,427,103- No/S LOC283755, 20,335,459Error! POTE15, Hyperlink OR4M2, reference OR4N4 not valid. Gain 183,903  48,583,127- Yes/S TRPM7,  48,767,030  USP50 Loss 83,750  47,643,250- No/S ZNF630,  47,727,000  SSX6 32 Loss 509,800  90,919,200- Yes/NS MTERF, SK  91,429,000  AKAP9, CYP51A1, LOC401387 Gain 211,000 112,463,000- No/NS KIAA1958, 112,674,000  C9orf80 Gain 124,800  47,030,100- No/NS No known  47,154,900  genes Gain 186,000 105,829,000- No/NS No known 106,015,000  genes Loss 888,000 112,325,000- Yes/NS No known 113,213,000  genes

Affymetrix GeneChip Human Mapping 500K Array Set

For each sample, approximately 500,000 SNPs were genotyped using the combined two-chip Nspl and Styl GeneChip® Human Mapping Commercial or Early Access Arrays (Affymetrix, Inc., Santa Clara, Calif.) according to the manufacturer's instructions and as described previously (Kennedy et al. 2003 Nat Biotechnol. 21:1233-7, the contents of which are incorporated herein by reference). Briefly, 250 ng of genomic DNA was digested with Nspl and Styl restriction enzyme (New England Biolabs, Boston, Mass.), ligated to an adaptor and amplified by PCR. The PCR products were then fragmented with DNasel to a size range of 250 bp to 2,000 bp, labelled, and hybridized to the array. After hybridization, arrays were washed on the Affymetrix fluidics stations, stained, and scanned using the Gene Chip Scanner 3000 7G and Gene Chip Operating System. Data has been submitted to the Gene Expression Omnibus database (accession GSE9222). Karyotypes were generated using standard clinical diagnostic protocols.

Characterization of Copy Number Variation

Nspl and Styl array scans were analyzed for copy number variation using a combination of DNA Chip Analyzer (dChip) (Li and Wong 2001 Genome Biology 2: 0032.1-0032.11), Copy Number Analysis for GeneChip (CNAG) (Nannya 2005 Cancer Res. 65:6071-9) and Genotyping Microarray based CNV Analysis (GEMCA) (Komura 2006 Genome Res. 16:1575-84). Each of these references is incorporated herein by reference.

Analysis with dChip (www.dchip.org) was performed as previously described (Zhao et al 2005 Cancer Res. 65:5561-70) in batches of ˜100 probands. Briefly, array scans were normalized at the probe intensity level with an invariant set normalization method. After normalization, a signal value was calculated for each SNP using a model-based (PM/MM) method. In this approach, image artifacts were identified and eliminated by an outlier detection algorithm. For both sets of arrays, the resulting signal values were averaged across all samples for each SNP to obtain the mean signal of a diploid genome. From the raw copy numbers, the inferred copy number at each SNP was estimated using a Hidden Markov Model (HMM).

For analyses with CNAG version 2.0 (www.genome.umin.jp), the reference pool was set to include all samples and performed an automatic batch pair-wise analysis using sex-matched controls. Test samples were compared to all samples within the reference pool and matched based on signal intensity standard deviations. The scan intensities for each ‘test’ sample were compared to the average intensities of the reference samples (typically the average of 5-12 samples) and used to calculate raw copy number changes. Underlying copy number changes were then inferred using a Hidden Markov Model (HMM) built into CNAG.

GEMCA analysis was performed essentially as described (Komura et al. Genome Res 2006; 16(12):1575-84) with the exception that two designated DNA samples (NA10851 and NA15510) were used as references for pair-wise comparison to all proband experiments. These results were further filtered by only including those CNVs that were common to both pair-wise experiments.

CNVs were merged if they were detected in the same individual by more than one algorithm using the outside probe boundaries.

Controls and Autism Chromosome Rearrangement Database (ACRD)

Control samples consisted of (i) CNVs observed in 500 Europeans from the from the German PopGen project (Krawczak et al. Community Genet 2006; 9(1):55-61), and CNVs found in a cohort of 1000 Caucasian non-disease controls from the Ontario population (ref. 24). The ACRD that had 834 putative CNVs or breakpoints mapped to the genome was established. A CNV was considered ASD-specific if it was >10 kb, contained at least three probes and at least 20% of its total length was unique when compared to controls.

CNV Validation Experiments and Balance Rearrangement Breakpoint Mapping

PCR validation of CNV calls was performed using Quantitative Multiplex PCR of short fluorescent fragments (QMPSF) (Redon et al. Nature. 444:444-54) or SYBR-Green 1 based real-time quantitative PCR (qPCR) using controls at the ACCNJ, CFTR or FOXP2 loci (PMID: 14552656). For both methods, primers were designed using the program PRIMER3 (http://frodo.wi.mit.edu/). Balanced rearrangements were mapped primarily using FISH (Nannya et al. Cancer Res 2005; 65(14):6071-9). The microdel program (Komura et al., ibid) was used to score CNV losses.

For QMPSF, short genomic sequences (140-220 bp) within putative CNVs were PCR amplified using dye-labelled primers corresponding to unique sequences. Each reaction also included co-amplified control amplicons corresponding to either ACCN1 or CFTR located at 17q11.2 and 7q31.2, respectively. Briefly, 40 ng of genomic DNA was amplified by PCR in a final volume of 25 μl using AmpliTaq® DNA polymerase (manufactured for Applied Biosystems by Roche Molecular Systems, Inc.) After an initial step of denaturation at 95° C. for 5 minutes conditions were as follows: 25 PCR cycles of 94° C. for 30 seconds, annealing at 60° C. for 45 seconds, and extension at 72° C. for 30 seconds. A final extension step at 72° C. for 15 minutes followed. QMPSF amplicons were separated on an ABI 3730x1 DNA Analyzer (Applied Biosystems, Foster City, Calif.), and analyzed using ABI GeneMapper® software version 3.7 (Applied Biosystems). After adjustment of control amplicons to the same heights, the QMPSF pattern generated from test DNA was superimposed to that of the control DNA. For each putative CNV locus, the copy number ratio was determined by dividing the normalized peak height obtained from the test DNA by that of the control DNA. Peak ratios of >1.4 and <0.7 were indicative of copy number gains and losses, respectively. At least two independent QMPSF assays were required for CNV confirmation.

SYBR Green I-based real-time qPCR amplification was performed using a Mx3005P quantitative PCR system (Stratagene, La Jolla, USA). Non-fluorescent primers were designed to amplify short genomic fragments (<140 bp) in putative CNV loci. Each assay also included amplification of a control amplicon corresponding to FOXP2 at 7q31.1 for comparison. After optimization of primer sets with control genomic DNA using ‘Brilliant® SYBR® Green QPCR Master Mix’ (Stratagene), test samples were assayed in 15 μl reaction mixtures in 96-well plates containing: 7.5 μl of reaction mix, 1.8 μl of primer, 6.0 ng of genomic DNA at 1.2 ng/μl, 0.225 μl of reference dye with 1:500 dilution, and 0.475 μl of water. PCR conditions consisted of 10 minutes of polymerase activation at 95° C., followed by 40 cycles of: 95° C. for 15 seconds and a single step at 60° C. for 1 minute for annealing and elongation. These steps were then followed by a final cycle of 95° C. for 1 minute, 55° C. for 30 seconds, and 95° C. for 30 seconds. Standard curve quantification was analyzed by MxPro-Mx3005P software (version 3.20 Build 340) to calculate copy number changes. Coefficient of variation (CV) was calculated on all sample Ct values to remove possible outlier when CV was greater than 1%. The average quantity of the putative CNV locus was divided by the average quantity of the control amplicon on FOXP2. Ratios of >1.4 and <0.7 were indicative of copy number gains and losses, respectively. Each putative CNV locus had at least two independent assays.

Results Structural Variation Characteristics in ASD Cases

A total of 426 ASD index cases were tested for CNV content including 394 typical idiopathic cases and 32 others that were enrolled based on prior knowledge of having a cytogenetic abnormality. The Affymetrix 500 k SNP array was used because it provided the highest resolution screen available for both SNP genotype and CNV data. Using the SNPs, the ancestry of each sample was categorized (to guide selection of controls). Backgrounds of the samples were found to be: 90.3%, 4.5%, 4.5%, and 0.7%, European, European/mixed, Asian, or Yoruban, respectively.

To maximize CNV discovery, three calling algorithms were used as described above (see FIG. 1) and common results between them were merged to identify a ‘full’ dataset of 3389 independent CNVs (˜8 CNVs per genome, mean size 390 kb) (see Table 4 below). To minimize potential false positives, a second dataset was generated whereby a CNV needed to be detected by two or more algorithms and/or on both the NspI or StyI microarrays (Pinto et al. Hum Mol Genet 2007; 16 Spec No 2:R168-73).

This ‘stringent’ dataset contained 1312 CNVs (˜3 CNVs per genome, mean size 603 kb). Using q-PCR, 48% (12/26) and 96% (48/50) of random CNVs were validated in the full and stringent collections, respectively.

TABLE 4 Summary of CNV in ASD and Controls POPGEN CONTROLS AUTISM PROBANDS All CNVs All CNVs Autism Specific¹ Full Stringent² Full Stringent² Full Stringent² #samples 500 500 426 426 426 426 #CNVs 3695 1558 3389 1312 888 276 CNV/Genome³ 7.4 3.1 8.0 3.1 2.1 0.65 Mean/Median 315/151 470/224 390/162 603/219 518/121 1082/194  Size (kb) % Gain/Loss 59/41% 70/30% 58/42% 62/38% 61/39% 57/43% Overlapping 3005/333  1226/142  2728/277  980/94  397/122 30/13 CNV/Loci (%)⁴ (81%) (78%) (80%) (74%) (44%) (11%) >1 Mb CNV (%) 343 250 339 212 63 32 (9%) (16%) (10%) (16%) (7%) (12%) ¹Not seen in controls. ²Stringent dataset as called by >1 algorithms or arrays. Analysis with dChip was performed in batches of ~100 probands. For CNAG version 2.0, the reference pool was set to include all samples and performed an automatic batch pairwise analysis using sex-matched controls. For GEMCA two designated DNA samples (NA10851 and NA15510) were used as references for pairwise comparison to all proband experiments. These results were further filtered by only including those CNVs that were common to both pairwise experiments. In all instances CNVs were merged if they were detected in the same individual by more than one algorithm using the outside probe boundaries. ³CNV/genome breakdown by algorithm: dChip Merged (3.0/genome), CNAG Merged (5.6/genome), GEMCA (5.5/genome). Validation experiments using q-PCR and FISH are described in the text. Another form of validation comes from examining the trios where we can demonstrate inheritance in 48 (maternal is 25, paternal is 23) of the autism-specific stringent dataset. Also from the trios, 148 confirmed regions (inheritance assignment) in the stringent dataset that overlap with controls (maternal is 65, paternal is 83). ⁴Represents the total number of overlapping and/or recurrent CNVs, the number of overlapping/CNV loci, and the percentage of overlapping CNVs, out of the total dataset.

Five hundred European control samples were examined for their CNV content and similar numbers of CNVs (3695 in the full and 1558 in the stringent dataset) were found to those in the ASD cases (Table 4). This suggested germ-line chromosome instability was not a significant contributing mechanism. The ASD CNVs were then compared against the 500 European/Caucasian controls and the Database of Genomic Variants (a repository of structural variation in ‘non-disease’ populations) (Iafrate et al. Nat Genet 2004; 36(9):949-51) to establish autism-specific CNV datasets. The subsequent analysis then focused on the 276 CNVs in the stringent autism-specific category, which mapped across all 23 chromosomes (FIG. 2), details of which are found in Table 3, below. Additional ASD-relevant CNV data is also found in the other categories in Table 5 (discussed below).

TABLE 3 FAM ID (DNA) Sex Type Chr start stop size CNV CNV Category SK0215-006 (58449) M CHR 1 97,271,600 98,364,100 1,092,500 loss CNVs confirmed de novo SK0152-003 (41548L) M CHR 3 15,125,800 16,535,400 1,409,600 loss CNVs confirmed de novo SK0181-003 (52191) M CHR 3 65,286,300 70,633,200 5,346,900 loss CNVs confirmed de novo SK0205-004 (56242) F CHR 5 81,949 13,882,933 13,800,984 loss CNVs confirmed de novo SK0152-003 (41548L) M CHR 5 9,275,811 12,705,200 3,429,389 loss CNVs confirmed de novo SK0083-003 (50800L) M CHR 7 108,200,381 119,223,887 11,023,507 loss CNVs confirmed de novo SK0131-003 (39989) F CHR 7 113,335,000 128,821,721 15,486,722 loss CNVs confirmed de novo SK0262-003 (68609) M SPX 8 710,491 1,501,580 791,089 gain CNVs confirmed de novo SK0152-003 (41548L) M CHR 12 40,584,198 41,007,040 422,842 loss CNVs confirmed de novo MM0278-003 (57788) M SPX 12 114,170,000 132,388,000 18,218,001 gain CNVs confirmed de novo SK0243-003 (67941) M CHR 15 69,601,300 73,890,800 4,289,500 loss CNVs confirmed de novo NA0067-000 (65344L) M SPX 16 87,800,593 88,066,260 265,668 loss CNVs confirmed de novo SK0218-003 (60340) F CHR 18 55,756,601 76,115,600 20,358,999 loss CNVs confirmed de novo MM0109-003 (46486) F SPX 20 60,949,339 62,377,000 1,427,662 gain CNVs confirmed de novo SK0244-003 (69183) M SPX 21 42,974,148 43,328,084 353,936 gain CNVs confirmed de novo NA0039-000 (69736) F CHR 22 46,277,400 49,509,100 3,231,700 loss CNVs confirmed de novo MM0109-003 (46486) F SPX 22 49,243,247 49,519,949 276,703 loss CNVs confirmed de novo NA0097-000 (82361L) F CHR X 34,419 5,859,730 5,825,312 loss CNVs confirmed de novo SK0306-004 (78681) F SPX X 48,073,600 52,716,966 4,643,367 gain CNVs confirmed de novo SK0147-003 (47544L) F SPX 2 114,855,796 115,334,166 478,371 loss CNVs Recurrent/Overlap SK0167-003 (60966L) F MPX 2 114,855,796 115,334,166 478,371 gain CNVs Recurrent/Overlap SK0288-003 (75420) F SPX-MZ 2 115,141,880 115,247,000 105,121 gain CNVs Recurrent/Overlap NA0030-000 (55240) M SPX 2 186,674,000 186,786,323 112,324 loss CNVs Recurrent/Overlap SK0306-004 (78681) F SPX 2 186,674,000 186,771,130 97,131 loss CNVs Recurrent/Overlap MM0220-003 (61180L) M MPX 6 118,799,000 119,117,000 318,001 gain CNVs Recurrent/Overlap NA0025-000 (60490) M SPX 6 118,823,011 119,117,000 293,990 gain CNVs Recurrent/Overlap SK0190-003 (54742) M SPX 7 152,698,000 154,478,000 1,780,000 gain CNVs Recurrent/Overlap SK0115-003 (40555) M SPX 7 153,098,000 153,372,000 274,001 gain CNVs Recurrent/Overlap SK0058-003 (59963) M MPX 7 153,539,745 153,556,533 16,789 gain CNVs Recurrent/Overlap SK0143-003 (36812) M SPX 8 53,481,200 53,766,400 285,201 gain CNVs Recurrent/Overlap MM0236-004 (46475) M MPX 8 53,724,445 53,996,124 271,680 gain CNVs Recurrent/Overlap SK0270-003 (71341) M SPX 9 7,725,280 7,764,180 38,900 loss CNVs Recurrent/Overlap MM0103-003 (42387) M MPX 9 7,725,283 7,760,233 34,951 loss CNVs Recurrent/Overlap MM0272-003 (45563) M MPX 11 40,285,800 40,548,738 262,939 loss CNVs Recurrent/Overlap SK0167-003 (60966L) F MPX 11 40,417,554 40,610,400 192,847 loss CNVs Recurrent/Overlap SK0023-003 (58096) M SPX 13 66,470,851 66,660,289 189,438 gain CNVs Recurrent/Overlap MM0299-003 (51674) F MPX 13 66,487,899 66,660,300 172,402 gain CNVs Recurrent/Overlap MM0109-003 (46486) F SPX 16 21,441,805 22,688,093 1,246,289 gain CNVs Recurrent/Overlap MM0289-003 (42267) F MPX 16 21,808,808 22,611,363 802,556 loss CNVs Recurrent/Overlap MM0088-003 (45562) F MPX 16 29,559,989 30,235,818 675,830 loss CNVs Recurrent/Overlap NA0133-000 (78119L) F SPX 16 29,559,989 30,085,308 525,320 gain CNVs Recurrent/Overlap SK0091-004 (46407) F MPX 22 17,265,500 21,546,762 4,281,262 gain CNVs Recurrent/Overlap SK0323-003 (80022) M MPX 22 18,683,900 19,427,000 743,101 gain CNVs Recurrent/Overlap SK0123-004 (60536L) M MPX 22 47,717,300 48,318,828 601,528 gain CNVs Recurrent/Overlap MM0102-003 (47598) M MPX 22 48,152,289 48,232,669 80,380 loss CNVs Recurrent/Overlap CNVs Recurrent/Overlap NA0002-000 (52026) M SPX 7 153,585,000 153,651,462 66,463 loss CNVs confirmed de novo CNVs Recurrent/Overlap SK0073-003 (57283L) F CHR 15 18,376,200 30,298,800 11,922,600 gain CNVs confirmed de novo CNVs Recurrent/Overlap SK0245-005 (68517) M CHR 15 18,427,100 30,298,847 11,871,747 gain CNVs confirmed de novo CNVs Recurrent/Overlap SK0119-003 (35190) M MPX 22 17,014,900 19,786,200 2,771,300 loss CNVs confirmed de novo MM0109-003 (46486) F SPX 17 40,555,289 41,089,766 534,478 loss CNVs that are Singletons MM0240-003 (43743) F MPX 17 40,555,289 41,128,323 573,035 loss CNVs that are Singletons NA0074-000 (63358) M SPX 1 41,463,611 41,924,314 460,704 gain CNVs that are Singletons SK0036-003 (29186) F SPX 1 57,936,233 58,514,629 578,396 gain CNVs that are Singletons MM0236-004 (46475) M MPX 1 60,369,200 61,426,300 1,057,101 gain CNVs that are Singletons MM0020-004 (47838) M MPX 1 65,649,086 65,713,423 64,338 gain CNVs that are Singletons NA0076-000 (63624) M SPX 1 91,930,266 92,330,344 400,078 gain CNVs that are Singletons SK0174-003 (64379L) M SPX 1 108,046,000 108,246,283 200,284 loss CNVs that are Singletons SK0283-003 (72309) F CHR 1 148,095,537 149,547,463 1,451,926 gain CNVs that are Singletons MM0011-003 (60566L) M MPX 1 165,908,677 166,028,402 119,726 loss CNVs that are Singletons SK0132-003 (30661) M MPX 1 186,673,899 186,716,570 42,672 loss CNVs that are Singletons NA0109-000 (72873) M SPX 1 212,037,558 212,471,000 433,443 loss CNVs that are Singletons SK0183-004 (52217) M SPX 1 238,633,145 239,606,926 973,781 loss CNVs that are Singletons MM0219-003 (46823) M MPX 2 34,155,700 34,253,221 97,522 loss CNVs that are Singletons MM0295-003 (46488) M MPX 2 34,662,196 34,780,515 118,320 loss CNVs that are Singletons NA0083-000 (66104L) M SPX 2 34,858,330 34,937,455 79,125 loss CNVs that are Singletons SK0270-003 (71341) M SPX 2 39,992,374 40,053,300 60,926 loss CNVs that are Singletons NA0055-000 (59448) M SPX 2 41,958,200 42,088,448 130,249 loss CNVs that are Singletons SK0301-003 (77203) M MPX 2 52,856,046 52,969,575 113,530 loss CNVs that are Singletons NA0027-000 (60421L) M MPX 2 121,623,000 121,684,915 61,915 loss CNVs that are Singletons NA0057-000 (59537) M SPX 2 125,496,832 125,890,571 393,740 loss CNVs that are Singletons MM0176-003 (62118L) M MPX 2 135,358,000 135,471,070 113,071 loss CNVs that are Singletons SK0225-003 (60921) M SPX 2 155,849,451 155,988,560 139,109 loss CNVs that are Singletons SK0192-003 (54877) M SPX 2 181,771,621 181,944,065 172,445 loss CNVs that are Singletons NA0007-000 (50611) M SPX 2 195,170,000 195,217,247 47,248 gain CNVs that are Singletons SK0283-003 (72309) F CHR 3 5,365,506 5,409,964 44,458 loss CNVs that are Singletons MM0210-004 (47376) M MPX 3 7,957,390 8,250,541 293,151 gain CNVs that are Singletons NA0044-000 (57097) M SPX 3 35,613,300 35,928,200 314,901 gain CNVs that are Singletons SK0021-008 (51504) M MPX 3 36,110,965 36,215,909 104,945 loss CNVs that are Singletons MM0154-003 (56678L) F MPX 3 50,089,500 50,199,200 109,701 gain CNVs that are Singletons SK0152-003 (41548L) M CHR 3 78,902,000 78,957,000 55,000 gain CNVs that are Singletons NA0044-000 (57097) M SPX 3 82,866,400 84,544,763 1,678,364 gain CNVs that are Singletons SK0023-003 (58096) M SPX 3 99,400,957 99,484,400 83,443 gain CNVs that are Singletons NA0018-000 (72622) M SPX 3 117,838,700 117,937,000 98,301 gain CNVs that are Singletons NA0003-000 (48474) M SPX 3 124,386,373 124,456,000 69,628 gain CNVs that are Singletons NA0090-000 (65410) M SPX 3 183,837,706 183,940,069 102,364 gain CNVs that are Singletons NA0044-000 (57097) M SPX 4 55,718,164 55,811,710 93,547 loss CNVs that are Singletons NA0016-000 (51524L) F SPX 4 114,333,509 114,416,051 82,542 loss CNVs that are Singletons SK0012-003 (58468L) M SPX 4 152,993,000 153,381,007 388,008 gain CNVs that are Singletons SK0103-005 (42258) M SPX 4 157,615,000 157,683,000 68,000 gain CNVs that are Singletons NA0037-000 (69812) M SPX 4 179,692,000 179,865,679 173,680 gain CNVs that are Singletons MM0299-003 (51674) F MPX 4 181,968,784 182,095,665 126,882 loss CNVs that are Singletons SK0266-003 (68257) M SPX 4 183,466,000 183,517,000 51,000 loss CNVs that are Singletons SK0002-003 (50002) F CHR 5 14,940,400 15,179,500 239,100 gain CNVs that are Singletons NA0078-000 (63727) M MPX 5 25,125,371 25,450,672 325,302 gain CNVs that are Singletons NA0076-000 (63624) M SPX 5 37,409,881 37,778,834 368,953 gain CNVs that are Singletons SK0335-003 (72815) F CHR 5 38,534,384 38,807,002 272,619 loss CNVs that are Singletons MM0143-004 (47386) M MPX 5 110,440,484 110,471,180 30,697 gain CNVs that are Singletons NA0023-000 (60504L) F SPX 5 113,104,916 113,178,000 73,084 loss CNVs that are Singletons SK0118-003 (52027) M SPX 5 122,834,399 123,029,036 194,638 loss CNVs that are Singletons SK0077-003 (48226) M SPX 5 128,968,799 129,433,000 464,201 gain CNVs that are Singletons SK0300-003 (77447) M CHR 6 4,200,904 4,416,471 215,568 loss CNVs that are Singletons MM0212-004 (62223L) F MPX 6 17,505,095 17,703,208 198,114 gain CNVs that are Singletons MM0300-003 (47836) F MPX 6 27,827,354 28,119,631 292,278 gain CNVs that are Singletons MM0225-004 (60826) M MPX 6 69,929,900 70,278,043 348,144 gain CNVs that are Singletons SK0217-003 (59279) M SPX 6 112,679,982 112,776,094 96,112 gain CNVs that are Singletons SK0326-003 (81155) M SPX 6 137,930,847 138,011,644 80,798 gain CNVs that are Singletons MM0088-003 (45562) F MPX 7 2,922,139 2,964,895 42,757 loss CNVs that are Singletons NA0147-000 (77123L) M SPX 7 3,946,854 4,002,686 55,833 loss CNVs that are Singletons SK0049-004 (59987L) M MPX 7 11,526,500 11,560,300 33,800 gain CNVs that are Singletons SK0132-003 (30661) M MPX 7 20,242,925 20,345,800 102,876 gain CNVs that are Singletons NA0145-000 (82058L) M SPX 7 47,742,927 48,775,200 1,032,274 loss CNVs that are Singletons SK0119-003 (35190) M MPX 8 17,706,313 17,738,524 32,211 loss CNVs that are Singletons SK0262-003 (68609) M SPX 8 18,623,000 19,442,500 819,500 gain CNVs that are Singletons SK0077-003 (48226) M SPX 8 42,971,601 43,820,300 848,699 gain CNVs that are Singletons SK0294-003 (76222) M SPX 8 73,762,894 73,798,241 35,348 gain CNVs that are Singletons SK0076-003 (38712) F SPX 8 83,989,256 84,141,278 152,022 gain CNVs that are Singletons MM0241-004 (45547) M MPX 8 87,230,811 87,498,988 268,178 gain CNVs that are Singletons MM0210-004 (47376) M MPX 8 104,166,572 104,947,190 780,618 gain CNVs that are Singletons SK0194-003 (55078) M SPX 8 123,539,127 123,644,422 105,296 loss CNVs that are Singletons SK0292-003 (75896) F MPX 8 130,467,000 130,529,193 62,194 loss CNVs that are Singletons MM0007-003 (59978) M MPX 9 5,099,530 5,235,490 135,961 gain CNVs that are Singletons MM0711-003 (63583L) M MPX 9 16,092,066 16,379,100 287,035 gain CNVs that are Singletons SK0015-003 (49932) M MPX 9 19,284,100 19,511,500 227,400 gain CNVs that are Singletons SK0015-003 (49932) M MPX 9 19,702,200 24,674,100 4,971,900 loss CNVs that are Singletons SK0278-003 (74431) M SPX 9 22,626,541 22,747,714 121,174 loss CNVs that are Singletons SK0148-005 (41350) F SPX 9 24,607,036 24,682,114 75,078 loss CNVs that are Singletons MM0020-004 (47838) M MPX 9 25,439,100 25,535,000 95,901 loss CNVs that are Singletons NA0105-000 (72085) M SPX 9 33,054,336 33,294,800 240,465 gain CNVs that are Singletons NA0147-000 (77123L) M SPX 9 84,957,060 85,054,672 97,613 loss CNVs that are Singletons SK0045-003 (58937) M MPX 9 109,446,000 109,837,000 391,000 gain CNVs that are Singletons MM0117-003 (59983) M MPX 10 2,313,505 2,407,102 93,598 loss CNVs that are Singletons MM0225-004 (60826) M MPX 10 4,976,040 5,124,511 148,472 gain CNVs that are Singletons MM1086-004 (76285) M MPX 10 31,256,118 31,604,509 348,392 loss CNVs that are Singletons MM0068-003 (60836) M MPX 10 68,139,200 68,246,027 106,828 loss CNVs that are Singletons NA0037-000 (69812) M SPX 10 104,641,000 104,786,777 145,778 loss CNVs that are Singletons SK0300-003 (77447) M CHR 11 6,845,440 6,899,830 54,391 loss CNVs that are Singletons SK0322-003 (79950) M SPX 11 33,159,190 33,462,070 302,881 gain CNVs that are Singletons MM0305-003 (47607) M MPX 11 68,053,777 68,204,900 151,123 gain CNVs that are Singletons NA0032-000 (55186) M SPX 11 76,114,600 76,140,500 25,900 gain CNVs that are Singletons MM0212-004 (62223L) F MPX 11 99,148,202 99,289,243 141,042 loss CNVs that are Singletons SK0167-003 (60966L) F MPX 11 101,131,785 101,246,901 115,117 loss CNVs that are Singletons MM0112-005 (46736) M MPX 11 116,789,980 116,855,347 65,368 gain CNVs that are Singletons MM0240-003 (43743) F MPX 11 117,452,000 117,539,000 87,001 gain CNVs that are Singletons SK0255-003 (68785) M SPX 11 124,303,460 124,719,976 416,517 gain CNVs that are Singletons NA0065-000 (62798L) M SPX 11 125,639,908 126,102,027 462,120 gain CNVs that are Singletons NA0172-000 (80993L) M SPX 12 3,727,911 3,879,230 151,320 loss CNVs that are Singletons SK0059-003 (29224) M SPX 12 10,431,082 10,445,300 14,218 gain CNVs that are Singletons SK0326-003 (81155) M SPX 12 46,170,200 46,365,774 195,575 gain CNVs that are Singletons SK0110-003 (24626) M SPX 12 50,520,400 50,573,516 53,116 gain CNVs that are Singletons NA0071-000 (64719L) F SPX 12 57,408,270 58,532,356 1,124,087 gain CNVs that are Singletons SK0305-003 (78621) F SPX 12 77,239,265 77,364,400 125,136 loss CNVs that are Singletons SK0301-003 (77203) M MPX 12 83,388,935 83,428,800 39,866 gain CNVs that are Singletons NA0093-000 (66999) M SPX 12 96,496,784 96,568,500 71,716 loss CNVs that are Singletons MM0711-003 (63583L) M MPX 12 96,576,486 96,639,686 63,201 loss CNVs that are Singletons SK0292-003 (75896) F MPX 12 101,568,000 101,586,000 18,001 gain CNVs that are Singletons NA0109-000 (72873) M SPX 12 110,646,607 110,800,000 153,394 gain CNVs that are Singletons MM0210-004 (47376) M MPX 12 125,446,000 125,757,000 311,000 gain CNVs that are Singletons SK0079-003 (48388) M MPX 13 17,960,300 18,492,994 532,694 gain CNVs that are Singletons NA0028-000 (58891L) M SPX 13 62,915,912 62,977,748 61,837 loss CNVs that are Singletons SK0326-003 (81155) M SPX 13 89,726,966 90,134,219 407,254 gain CNVs that are Singletons NA0048-000 (58569) M SPX 13 93,288,520 93,344,600 56,081 gain CNVs that are Singletons SK0326-003 (81155) M SPX 13 93,497,400 93,732,931 235,532 gain CNVs that are Singletons SK0254-003 (68687) M SPX 13 105,172,000 105,357,000 185,000 gain CNVs that are Singletons SK0121-003 (41288) M SPX 14 76,007,842 76,924,400 916,558 gain CNVs that are Singletons SK0031-003 (68160L) M CHR 14 99,015,100 99,787,500 772,400 gain CNVs that are Singletons SK0300-003 (77447) M CHR 15 48,583,127 48,767,030 183,904 gain CNVs that are Singletons SK0326-003 (81155) M SPX 15 97,406,000 97,961,522 555,523 gain CNVs that are Singletons SK0281-003 (72934) M SPX 16 57,542,779 57,579,900 37,122 loss CNVs that are Singletons MM0310-005 (60951) M MPX 16 80,972,252 80,983,135 10,884 loss CNVs that are Singletons SK0203-004 (56040) M MPX 16 82,603,600 82,687,900 84,300 gain CNVs that are Singletons SK0085-004 (30422) M MPX 17 3,836,592 3,998,867 162,276 gain CNVs that are Singletons SK0298-003 (77697) M SPX 17 76,914,079 77,771,141 857,063 gain CNVs that are Singletons SK0328-003 (82302) M SPX 18 13,794,043 14,743,900 949,858 gain CNVs that are Singletons SK0303-003 (78391) F MPX 18 28,383,551 28,448,100 64,550 loss CNVs that are Singletons SK0014-003 (41606) M SPX 18 52,531,252 53,165,421 634,169 gain CNVs that are Singletons SK0121-003 (41288) M SPX 19 33,693,363 33,762,805 69,442 loss CNVs that are Singletons NA0111-000 (73891) M SPX 19 57,836,600 58,246,200 409,601 gain CNVs that are Singletons NA0004-000 (47490) M SPX 19 58,634,965 58,958,584 323,620 gain CNVs that are Singletons NA0070-000 (64249L) F SPX 19 60,499,398 60,742,656 243,259 loss CNVs that are Singletons SK0047-003 (47173L) F SPX 19 61,910,800 62,644,900 734,100 loss CNVs that are Singletons NA0110-000 (72165) M SPX 19 63,050,356 63,193,800 143,445 loss CNVs that are Singletons SK0232-003 (59838) M MPX 19 63,483,000 63,771,100 288,100 gain CNVs that are Singletons MM0018-003 (59980) M MPX 20 11,319,093 11,424,900 105,808 loss CNVs that are Singletons SK0335-003 (72815) F CHR 20 14,955,730 15,011,214 55,485 loss CNVs that are Singletons SK0258-004 (67930) M SPX 20 45,468,000 45,673,300 205,300 gain CNVs that are Singletons MM0126-003 (54581) M MPX 21 22,839,570 22,938,377 98,808 loss CNVs that are Singletons SK0118-003 (52027) M SPX 21 28,060,406 28,250,400 189,995 loss CNVs that are Singletons SK0186-004 (52964) M SPX X 22,962,800 23,119,000 156,200 loss CNVs that are Singletons MM0087-003 (59962L) M MPX X 25,516,263 25,620,400 104,138 loss CNVs that are Singletons NA0100-000 (70601L) M SPX X 44,395,900 45,060,800 664,901 gain CNVs that are Singletons SK0087-003 (60692L) F MPX X 83,866,300 92,175,100 8,308,800 loss CNVs that are Singletons MM0020-004 (47838) M MPX X 87,452,050 87,595,200 143,151 gain CNVs that are Singletons SK0228-003 (62083) M SPX X 104,153,000 104,638,000 485,000 gain CNVs that are Singletons SK0088-003 (64798) M SPX X 114,042,922 114,215,435 172,513 gain CNVs that are Singletons MM0087-003 (59962L) M MPX X 130,406,000 130,695,499 289,500 gain CNVs that are Singletons NA0016-000 (51524L) F SPX X 140,600,370 140,907,495 307,125 gain CNVs that are Singletons SK0234-003 (64340) M MPX X 142,561,000 142,682,000 121,000 loss CNVs that are Singletons SK0320-003 (79449) M MPX X 143,059,574 143,399,300 339,727 gain CNVs that are Singletons SK0123-004 (60536L) M MPX X 147,974,000 148,479,449 505,449 gain CNVs that are Singletons SK0278-003 (74431) M SPX 1 188,543,244 188,935,335 392,092 gain CNVs that overlap ACRD MM0149-003 (42382) M MPX 1 191,030,551 191,223,110 192,560 gain CNVs that overlap ACRD SK0229-003 (62211) M SPX 1 242,451,000 243,113,489 662,489 gain CNVs that overlap ACRD NA0016-000 (51524L) F SPX 1 243,172,012 243,301,056 129,044 gain CNVs that overlap ACRD MM0063-003 (46687) F MPX 2 50,780,202 50,859,200 78,999 loss CNVs that overlap ACRD SK0234-003 (64340) M MPX 2 54,171,783 54,345,700 173,917 gain CNVs that overlap ACRD SK0188-003(53664) M SPX 2 112,415,581 112,510,212 94,632 loss CNVs that overlap ACRD MM0019-003 (42052) M MPX 2 201,286,000 201,317,066 31,067 loss CNVs that overlap ACRD MM0296-003 (47829) M MPX 2 221,429,610 221,551,000 121,391 loss CNVs that overlap ACRD NA0004-000 (47490) M SPX 2 235,797,267 236,239,000 441,734 gain CNVs that overlap ACRD MM0068-003 (60836) M MPX 3 1,720,948 1,795,234 74,287 gain CNVs that overlap ACRD NA0067-000 (65344L) M SPX 3 61,075,295 61,581,100 505,806 gain CNVs that overlap ACRD MM0296-003 (47829) M MPX 4 328,851 542,862 214,012 gain CNVs that overlap ACRD MM0228-004 (47602) M MPX 4 11,820,924 11,983,053 162,130 loss CNVs that overlap ACRD NA0129-000 (77405) M SPX 4 38,109,899 38,349,444 239,546 gain CNVs that overlap ACRD SK0188-003 (53664) M SPX 4 61,408,094 61,758,800 350,707 loss CNVs that overlap ACRD SK0057-003 (40919) M SPX 4 74,105,700 74,464,300 358,600 gain CNVs that overlap ACRD MM0176-003 (62118L) M MPX 4 91,220,121 91,309,602 89,482 loss CNVs that overlap ACRD SK0012-003 (58468L) M SPX 4 162,387,402 163,362,655 975,254 gain CNVs that overlap ACRD SK0012-003 (58468L) M SPX 4 173,324,616 174,954,056 1,629,441 gain CNVs that overlap ACRD SK0166-003 (36773) M SPX 4 186,788,000 187,118,000 330,001 gain CNVs that overlap ACRD SK0074-003 (60910L) M MPX 4 188,230,567 190,154,000 1,923,434 gain CNVs that overlap ACRD SK0083-003 (50800L) M CHR 4 188,232,000 188,253,314 21,315 gain CNVs that overlap ACRD MM0019-003 (42052) M MPX 4 190,172,765 191,306,043 1,133,279 gain CNVs that overlap ACRD SK0188-003 (53664) M SPX 5 13,832,700 14,237,600 404,901 gain CNVs that overlap ACRD NA0078-000 (63727) M MPX 5 79,336,190 79,613,516 277,327 loss CNVs that overlap ACRD NA0145-000 (82058L) M SPX 5 89,445,869 90,172,900 727,032 gain CNVs that overlap ACRD SK0167-003 (60966L) F MPX 5 120,343,925 120,474,000 130,076 gain CNVs that overlap ACRD NA0019-000 (64122L) M SPX 5 120,964,000 121,095,213 131,214 gain CNVs that overlap ACRD MM0215-004 (47095) M MPX 5 132,619,430 132,732,003 112,574 loss CNVs that overlap ACRD SK0073-003 (57283L) F CHR 5 134,426,000 134,519,000 93,000 gain CNVs that overlap ACRD SK0272-003 (70721) F SPX 6 77,622,920 77,673,932 51,012 loss CNVs that overlap ACRD MM0225-004 (60826) M MPX 6 93,087,482 98,011,900 4,924,419 gain CNVs that overlap ACRD SK0077-003 (48226) M SPX 6 95,461,800 95,581,304 119,504 loss CNVs that overlap ACRD SK0087-003 (40450) M MPX 6 97,566,274 97,658,527 92,253 loss CNVs that overlap ACRD SK0216-003 (58875) M SPX 6 153,519,631 153,791,029 271,398 gain CNVs that overlap ACRD NA0061-000 (60383) M SPX 7 108,357,049 108,597,525 240,477 loss CNVs that overlap ACRD SK0226-005 (61360) M SPX 7 118,462,717 118,679,189 216,473 loss CNVs that overlap ACRD MM0218-004 (45553) M MPX 8 89,598,961 89,678,800 79,840 loss CNVs that overlap ACRD SK0210-004 (57601) M MPX 9 28,577,800 29,218,800 641,000 loss CNVs that overlap ACRD SK0273-003 (71182) M MPX 9 70,739,231 70,870,084 130,854 loss CNVs that overlap ACRD SK0118-003 (52027) M SPX 9 111,652,000 112,212,452 560,453 gain CNVs that overlap ACRD NA0066-000 (64119L) M SPX 9 116,528,784 116,612,329 83,546 loss CNVs that overlap ACRD SK0102-004 (31899) M SPX 10 42,611,900 43,266,300 654,400 gain CNVs that overlap ACRD SK0102-004 (31899) M SPX 10 44,988,900 45,468,800 479,900 gain CNVs that overlap ACRD NA0109-000 (72873) M SPX 10 112,267,330 112,405,408 138,079 gain CNVs that overlap ACRD SK0131-003 (39989) F CHR 10 128,501,014 128,592,091 91,078 gain CNVs that overlap ACRD NA0138-000 (81816L) M SPX 10 133,285,000 133,604,999 320,000 gain CNVs that overlap ACRD NA0113-000 (82366L) M SPX 11 9,984,119 10,667,800 683,682 loss CNVs that overlap ACRD SK0218-003 (60340) F CHR 12 1,760,084 1,852,412 92,328 loss CNVs that overlap ACRD NA0122-000 (76018L) F SPX 13 32,965,700 33,137,655 171,956 gain CNVs that overlap ACRD NA0117-000 (73621) M SPX 13 42,511,458 42,599,200 87,743 gain CNVs that overlap ACRD MM0154-003 (56678L) F MPX 13 54,651,953 55,025,229 373,277 gain CNVs that overlap ACRD SK0328-003 (82302) M SPX 13 103,896,769 103,930,492 33,724 loss CNVs that overlap ACRD MM0295-003 (46488) M MPX 13 113,361,712 113,646,000 284,289 gain CNVs that overlap ACRD SK0305-004 (78621) F SPX 14 42,022,286 42,210,026 187,741 loss CNVs that overlap ACRD SK0320-003 (79449) M MPX 14 45,537,581 45,653,418 115,838 loss CNVs that overlap ACRD MM0225-004 (60826) M MPX 14 83,373,278 83,435,200 61,923 gain CNVs that overlap ACRD MM0154-003 (56678L) F MPX 14 106,223,861 106,356,482 132,622 gain CNVs that overlap ACRD NA0064-000 (63582L) M SPX 15 82,573,421 83,631,697 1,058,276 loss CNVs that overlap ACRD MM0256-004 (46991) M MPX 15 87,922,400 87,993,909 71,510 gain CNVs that overlap ACRD SK0266-003 (68257) M SPX 16 6,813,789 6,898,849 85,060 loss CNVs that overlap ACRD NA0063-000 (60351) M SPX 16 73,397,667 73,657,067 259,400 loss CNVs that overlap ACRD NA0095-000 (75414L) M SPX 16 74,576,356 74,613,000 36,645 loss CNVs that overlap ACRD SK0284-003 (72687) F SPX 17 28,985,300 29,960,700 975,400 gain CNVs that overlap ACRD SK0012-003 (58468L) M SPX 18 27,565,032 27,781,900 216,869 gain CNVs that overlap ACRD SK0152-003 (41548L) M CHR 18 32,174,061 32,990,975 816,914 loss CNVs that overlap ACRD SK0147-003 (47544L) F SPX 18 37,509,556 37,950,450 440,895 gain CNVs that overlap ACRD SK0304-003 (78063) M SPX 18 46,101,841 46,218,000 116,160 gain CNVs that overlap ACRD NA0138-000 (81816L) M SPX 18 69,282,461 69,330,584 48,124 loss CNVs that overlap ACRD SK0023-003 (58096) M SPX 21 46,497,675 46,678,820 181,145 gain CNVs that overlap ACRD NA0112-000 (72340) M SPX X 38,250,331 38,371,333 121,003 gain CNVs that overlap ACRD SK0283-003 (72309) F CHR 4 44,762,996 44,858,504 95,508 gain CNVs that overlap ACRD MM0010-005 (47372) M MPX 4 44,773,367 44,846,800 73,434 gain CNVs that overlap ACRD NA0093-000 (66999) M SPX 4 44,773,367 44,846,800 73,433 gain CNVs that overlap ACRD MM0109-003 (46486) F SPX 4 189,538,747 189,825,000 286,254 gain CNVs that overlap ACRD SK0112-003 (46100) M MPX 4 189,580,553 190,228,000 647,447 gain CNVs that overlap ACRD

Wide-ranging prevalence frequencies of cytogenetically detectable chromosomal abnormalities in ASD, and the inability of microarray scans to find balanced abnormalities, prompted karyotyping to be performed. Karyotyping (and FISH) also provided the ability to characterize the chromosomal context (e.g. ring chromosomes) of some of the CNV regions, something not possible using microarrays alone. Therefore, 313 unbiased idiopathic cases where blood was available were examined and 5.8% (18/313) cases were found to have balanced (11) or unbalanced (7) karyotypes (all unbalanced karyotypic changes (7) were also found by microarray analysis and are included in the CNV statistics). The genomic characteristics of all CNVs are shown in the Autism Chromosome Rearrangement Database (see FIG. 3). In this study, CNV loss and gain will typically equate to a standard deletion or duplication. In some cases a duplication of only part of a gene could lead to its disruption (Table 5), and there are also positional effects on gene expression to consider.

De novo, Overlapping/Recurrent, and Inherited Structural Variants

Structural variants found in ASD cases were initially prioritized to possibly be etiologic if they were not in controls and, (i) de novo in origin (25 cases) (see Table 5 below), (ii) overlapping (27 cases at 13 loci) in two or more unrelated samples (see Table 7 below), (iii) recurrent (same breakpoints) in two or more unrelated samples (four cases at two loci), (iv) or inherited (the remainder). In a proof of principle analysis, CNVs were found at known ASD loci: NLGN4 and 22q, 15q, SHANK3 and NRXN1 in categories i, ii, iii, and iv, respectively. ASD structural variants found in controls (eg. NRXN1) could also be involved.

TABLE 5 De Novo Rearrangements in ASD cases FamID (DNA)¹ Sex Type Chromosome² Size (bp)³ CNV Genes⁴ Phenotype Comments⁵  1 SK0181-004 (52191) M CHR (SPX) 3p14.1-3p13 (a) 5,346,900 loss 13 genes IQ = 107 t (6;14) (q13;q21) (k) N/A none 11 genes Dysmorphology  2 SK0152-003 (41548) M CHR (MPX)⁶ 3p25.1-p24.3 (a) 1,409,600 loss 12 genes IQ = unknown 5p15.31-p15.2 (a) 3,429,389 loss  8 genes 12q12 (a) 422,842 loss  4 genes t (5;7) (p15p13) (k) N/A none CDH18  3 SK0215-006 (58449) M CHR (SPX) 1p21.3 (a) 1,092,500 loss DPYD whole IQ = 38, SLI  4 SK0205-004 (56242) F CHR (SPX) 5p15.33-5p15.2 (k) 13,800,984 loss 46 genes IQ = unknown, Cri du chat  5 SK0083-003 (50800) M CHR (SPX) 7q31.1-q31.31 (k) 11,023,507 loss 25 genes IQ = 76  6 SK0131-003 (39989) F CHR (SPX) 7q31.1-q32.2 (k) 15,486,722 loss >50 genes  IQ = 95, SLI  7 SK0243-003 (67941) M CHR (SPX) 15q23-q24.2 (k) 4,289,500 loss >50 genes  IQ = unknown, SLI  8 SK0073-003 (57283) F CHR (SPX) 15q11.2-q13.3 (k) 11,922,600 gain >50 genes  IQ = unknown  9 SK0245-005 (68517) M CHR (SPX) 15q11.2-q13.3(k) 11,871,747 gain >50 genes  IQ = unknown 10 SK0218-003 (60340) F CHR (MPX)⁴ 18q21.32-18q23 (k) 20,358,999 loss >50 genes  IQ = unknown, seizures, dysmorphology 11 NA0039-000 (69736) F CHR (SPX) 22q13.31-q13.33 (k) 3,231,700 loss 41 genes IQ = unknown 12 NA0097-000 (82361) F CHR (SPX) Xp22.33-p22.31 (a) 5,825,311 loss 21 genes + NLGN4 IQ = unknown 13 SK0283-003 (72309) F CHR (SPX) 47, XX, ring chr1 (k) N/A gain >50 genes  IQ = 38 14 SK0133-003 (46012 M CHR (SPX) t (5;8;17) (q31.1; N/A none  5 genes IQ = unknown q24.1;q21.3) (k) 15 NA0002-000 (52026) M SPX 7q36.2 (a) 66,462 loss DPP6 exonic IQ = unknown 16 SK0262-003 (68609) M SPX 8p23.3 (a) 791,089 gain DLGAP2 exonic IQ = unknown 17 MM0278-003 (57788) M SPX 12q24.21-q24.33 (a) 18,218,000 gain >50 genes  IQ = 36 18 NA0067-000 (65344) M SPX 16q24.3 (a) 265,667 loss ANKRD11 exonic IQ = unknown 19 MM0088-003 (45562) F MPX 16p11.2 (a) 675,829 loss 28 genes IQ = 87 20 SK0102-004 (31899) M SPX 16p11.2 (a) 432,600 gain 24 genes IQ = 74, Epilepsy 21 SK0244-003 (69183) M SPX 21q22.3 (a) 353,936 gain  4 genes IQ = 80 22 MM0109-003 (46486) F SPX 20q13.33 (a) 1,427,661 gain 44 genes IQ = unknown 22q13.33 (a) 276,702 loss 13 genes + SHANK3 23 SK0119-003 (35190) M MPX⁴ 22q11.21 (a) 2,771,300 loss >50 genes  IQ = 58, VCF syndrome 24 SK0297-003 (76066) M SPX-MZ 22q11.21 (a) 4,281,262 gain >50 genes  IQ = 107, dysmorphology 25 SK0306-004 (78681) F SPX Xp11.23-11.22 (a) 4,643,367 gain >50 genes  IQ = 87 ¹Table is sorted based on family type. Probands with abnormal karyotypes (CHR) (1-14) are separated from probands belonging to simplex (SPX) and multiplex (MPX) families with normal karyotypes(15-25). ²De novo event detected by either karyotype (k) or microarray (a) ³De novo CNV/translocation has been confirmed by at least one of karyotype, FISH, or qPCR. CNV size is based on array results. The breakpoints have not been accurately defined, and CNVs may be smaller or larger than posted. ⁴When only a single gene is involved if the CNV intersects (suggesting it may disrupt the gene) the term ‘exonic’ is used and if the CNV encompasses the entire gene the term ‘whole’ is used. ⁵For multiplex families the de novo events were not detected in affected siblings. **comment on case 25 that is also in Table 3(see entry #2

TABLE 6 Recurrent and overlapping loci in ASD Chromosome FamID (DNA) Sex Type¹ Size (bp)² CNV Origin Genes³ Phenotype Comments  1 2q14.1 SK0147-003 (47544) F SPX   478,370 loss Paternal DPP10 exonic IQ = unknown, NF1 SK0288-003 (75420) F SPX-MZ   105,120 gain Paternal DPP10 intronic IQ = 83  2 2q32.1 SK0306-004 (78681) F SPX    97,130 loss Unknown None IQ = 87 NA0030-000 (55240) M SPX   112,323 loss Unknown None IQ = unknown  3 6q22.31 MM0220-003 (61180) M MPX   318,000 gain Paternal PLN, c6orf204 whole IQ = unknown NA0025-000 (60490) M SPX   293,989 gain Paternal PLN, c6orf204 whole IQ = unknown  4 7q36.2 SK0190-003 (54742) M SPX  1,780,000 gain Maternal DPP6 whole IQ = 82 SK0115-003 (40555) M SPX   274,000 gain Unknown DPP6 exonic IQ = unknown SK0058-003 (59963) M MPX    16,788 gain Maternal DPP6 intronic IQ = 111 NA0002-000 (52026) M SPX    66,462 loss De novo DPP6 exonic IQ = unknown  5 8q11.23 SK0143-003 (36812) M SPX   285,200 gain Unknown UNQ9433 whole, IQ = 66 RB1CC1 exonic Apraxia, CHD, Seizures MM0236-004 (46475) M MPX   271,679 gain Unknown RB1CC1 exonic IQ = 99  6 9p24.1 SK0270-003 (71341) M SPX    38,900 loss Unknown none IQ = 91, SLI MM0103-003 (42387) M MPX    34,950 loss Paternal none IQ = 107  7 11p12 MM0272-003 (45563) M MPX   262,938 loss Maternal none IQ = 111, Seizures SK0167-003 (60966) F MPX   192,846 loss Unknown none IQ = 91  8 13q21.32 SK0023-003 (58096) M SPX   189,438 gain Unknown PCDH9 intronic IQ = 91, Seizures MM0299-003 (51674) F MPX   172,401 gain Paternal PCDH9 intronic IQ = 39  9 15q11.2- SK0073-003 (57283) F CHR 11,922,600 gain De novo >50 genes IQ = unknown q13.3 SK0245-005 (68517) M CHR 11,871,747 gain De novo >50 genes IQ = unknown 10 16p12.1 MM0109-003 (46486) F SPX  1,246,288 gain Maternal 8 genes IQ = unknown MM0289-003 (42267) F MPX   802,555 loss Maternal 5 genes IQ = 63 11 16p11.1 NA0133-000 (78119) F SPX   525,319 gain Maternal 29 genes IQ = unknown SK0102-004 (31899) M SPX    432,600⁴ gain De novo 24 genes IQ = 64, Epilepsy MM0088-003 (45562) F MPX   675,829 loss De novo 32 genes IQ = 87 12 22q11.2 SK0119-003 (35190) M MPX  2,771,300 loss De novo >50 genes IQ = 58, VCF syndrome SK0091-004 (46407) F MPX  4,281,262 gain Paternal >50 genes IQ = 126 SK0297-003 (76066) M SPX-MZ  4,281,262 gain De novo >50 genes IQ = 107, dysmorphology SK0323-003 (80022) M MPX   743,100 gain Unknown 7 genes IQ = unknown 13 22q13.31 SK0123-004 (60536) M MPX   601,528 gain Maternal none IQ = 93 MM0102-003 (47598) M MPX    80,380 loss Maternal none IQ = 70 ¹Families are grouped based on simplex (SPX), multiplex (MPX) and chromosomal abnormalities (CHR). Simplex families with affected monozygotic twins is denoted as SPX-MZ. The de novo cases also appear in Table 2 and some of the family pedigrees are shown in FIG. 2 and Supplemental FIG. 2. ²CNV size is based on array results. The breakpoints have not been accurately defined, and CNVs may be smaller or larger than posted. ³When only a single gene is involved if the CNV intersects (suggesting it may disrupt the gene) the term ‘exonic’ is used and if the CNV encompasses the entire gene the term ‘whole’ is used. ⁴CNV is only called by one algorithm

By testing parental DNA and validating CNVs, a de novo mutation rate of 7.1% (4/56) and 2.0% (1/49) was observed in idiopathic simplex and multiplex families, respectively. There was parental information for 13 of 18 cases discovered to carry cytogenetic abnormalities and 7 (6 simplex, 1 multiplex) of these were de novo in origin. Since only 1/7 (from a simplex family) of these was balanced and directly interrupting a gene, it was estimated that this class of rearrangements had much less of a contribution than CNVs to the total rate of de novo and structural variation in the present cohort.

The collective data identified 25 de novo cases (Table 5) and in three, two or more events were identified. Notably, in family SK0152 (FIG. 4a ) there were four de novo events. In MM019 (FIG. 4b ) there were two de novo deletions, one leading to haplo-insufficiency of SHANK3.

The 13 loci where overlapping ASD-specific CNVs were found are likely indicative of ASD-susceptibility since they arise in two or more unrelated families. In six, gains and losses often encompassing entire genes were observed at the same locus (Table 6) suggesting general gene dysregulation to be involved.

Using q-PCR or by assessing SNP patterns, 196 inherited CNVs (90 maternal and 106 paternal) were confirmed. No sub-grouping of these demonstrated obvious parent-of-origin effects (the two chromosome 15q11-q13 duplications detected were both de novo in origin). A 160kb deletion was detected in a male inherited from a carrier mother, leading to a null PTCHD1 in the proband and his dizygotic twin brother (FIG. 4c ). There were also instances where apparently balanced inherited translocations were accompanied by de novo deletions in the offspring (eg. DPYD) (FIG. 4d ).

Candidate ASD-Susceptibility Genes and Loci Identified

New ASD candidates identified were those with a structural change (either de novo or found in two or more unrelated ASD cases, or for the X chromosome an allele being transmitted maternally from an unaffected carrier) specific to that gene, including ANKRD11, DLGAP2, DPP6, DPP10, DPYD, PCDH9 and PTCHD1 (Tables 5 and 6). As previously noted, NLGN4, SHANK3 and NRXN1 were also identified. The PCDH9 and NRXN1 genes are also found as CNVs in controls in the DGV (Database of Genomic Variants).

Additional positional candidate genes identified were those found interrupted by balanced cytogenetic breakpoints including NEGR1, PIP5K1B, GABRG1, KLHL3, STK3, ST7, SATB2 (Table 1). Moreover, 77 CNVs in the stringent dataset overlapped with the Autism Chromosome Rearrangement Database providing a second line of evidence for involvement (FIG. 2). For example, a 4.6 Mb de novo duplication at Xp11.23-11.22 was detected in a female SK0306-004 (Table 5) and a male in the database.

DPP6 and DPP10 emerge as being positional and functional candidates. DPP6 (˜1.5 Mb in size at 2q14.1) and DPP10 (˜1.3 Mb at 7q36.2) code for accessory trans-membrane dipeptidyl peptidase-like subunits that affect the expression and gating of Kv4.2 channels (KCND2). Kv4.2 channels function in regulation of neurotransmitter release and neuronal excitability in the glutamatergic synapse at the same sites where SHANK3 and the NLGN gene products are found. In addition, autism balanced breakpoints have been mapped near KCND2 at 7q31.

For DPP10 there are inherited CNV gains and losses (Table 5, FIG. 4). De novo and inherited CNVs were found at the multi-transcript DPP6 gene. A 66 kb de novo loss encompassing exons 2 and 3 is found in a male in family NA0002 (FIG. 4e ). In family SK0190, the male proband and an unaffected female sibling both carry a CNV gain inherited from an unaffected mother (FIG. 4f ) that encompassed the entire DPP6. A 270 kb gain was found in SK0115-003 that extends across the first exon (which may disrupt the functional gene) and SK0058-003 carries a maternally-inherited 16 kb intronic CNV gain (Table 1; FIG. 5).

Medical Genetics

Structural variants overlapping loci involved in medical genetic conditions including Waardenburg Type IIA (3p14.1), speech and language disorder (7q31), mental retardation (MR)(15q23-q24, 16p11.2) and velocardialfacial syndrome (VCFS) (22q13) were identified (Table 5), amongst others. Identification of the structural variant at these loci led to clinical re-assessment and either identification or refinement of the diagnosis, for additional syndromic features. Other instances (eg. SK0186-PTCHD1 deletion) (FIG. 4c ) prompted re-testing of the entire family and eventually a diagnosis of mild-ASD in a previously undiagnosed sibling. This family was then redesignated multiplex as opposed to simplex.

The identification of a de novo deletion (2.7 Mb) at 22q11.2 in two ASD brothers led to their re-examination and diagnosis for VCFS. The re-testing also further defined the siblings to be at opposite ends of the ASD spectrum (FIG. 6). Larger duplications (4.3 Mb) of this same region in two other ASD families (SK0289 and SK0091) did not cause VCFS (Table 6); however, in SK0091 the variant was inherited from a normal father and not found in an affected male sibling.

A recurrent ˜500 kb duplication at 16p11.2 in two ASD families (SK0102 and NA0133) (FIGS. 4 and 5) was also discovered. As with DPP6IDPP10 and 22q11.2, there were carriers of these structural variants without ASD. In a third family (MM0088), the proband has a larger 676 kb de novo deletion and it is only detected in one of two ASD siblings. (FIG. 4g ).

In sum, using the genome-wide scanning approach, numerous new putative-ASD loci (Tables 4 and 5, FIG. 2) were identified. Generally, ASD loci include (i) those that contain genes functioning in the PSD, (ii) and/or chromosomal regions previously shown to be involved in mental retardation, and (iii) involve dysregulation of gene expression.

CNVs that implicate ASD loci include the SHANK3, NLGN, and NRXN1-PSD genes and also identify novel loci at DPP6 and DPP10 (amongst others including PCDH9, RPS6KA2, RET from the full dataset) were identified.

Lastly, six unrelated ASD cases were identified (Table 6) that had either CNV gains or losses at the same locus which indicate that gene expression of genes in these regions are related to the development of speech and language and/or social communication in humans, as in SHANK3 and genes in the Williams-Beuren syndrome locus.

EXAMPLE 2 PTCHD1 as a Marker of ASD

As set out above, a genome scan with Affymetrix 500K SNP Arrays was used to identify a CNV deletion on chromosome Xp22.11 that spans exon 1 of the PTCHD1 gene. Exon 1 is shown bolded in FIG. 7 spanning nucleotide positions 1-359. The Cdna sequence of the PTCHD1 gene (NM_173495) as well as the amino acid sequence of the corresponding encoded protein is illustrated in FIG. 7 which illustrates a genomic size of: 59325, an exon/coding exon count of 3 encoding a protein of 783 amino acids.

The deletion was determined to be an ˜156 kb deletion on Xp22.11 on a male proband. The physical position of this CNV is chrX:22,962,800-23,119,000 (UCSC 2004 Assembly). The deletion is flanked by SNP probes rs7055928 and rs1918560 (at 22.956 and 23.133 Mb from the Xp terminus, respectively). The most proximal and distal SNPs (from the Affymetrix SNP microarrays) within the deleted region, as determined by the SNP microarray analysis, are rs7879064 (23.119Mb) and rs4828958(22.972 Mb). PCR amplicons from within the deleted region were used to confirm the deletion by Qper (PCR primers and locations are given below). This deletion spans the entire exon 1 of the PTCHD1 gene (NM_173495). Analysis of both Sty and Nsp chips data identified this event and was further validated using PCR and QPCR techniques. The following primers were used:

(SEQ ID NO: 1) PTCHD-CNV1F ATTCGCAGTTCCTTCGTCTT (SEQ ID NO: 2) PTCHD-CNV1R AAAGTGGATTGATCGGTTCC (SEQ ID NO: 3) PTCHD-CNV2F GCTTGAGGACGTGTTTCTCC (SEQ ID NO: 4) PTCHD-CNV2R CTAGGAGAGGTGGCGCTCT

This CNV is autism specific as it was not present in the Database of Genomic Variants (DGV) and in other controls. Furthermore, the segregation of this deletion was characterized in family and it was identified that the deletion was transmitted from a heterozygous mother. A male sibling also had language deficits.

Mutation screening of PTCHD1 in N=400 autism patients was conducted in the usual manner. The following primers were used:

(SEQ ID NO: 5) PTCHD1-x1F AGCGTGCGCCTCGCCCT (SEQ ID NO: 6) PTCHD1-x1R TCCTTGTCCAGGAGGCTGGGA (SEQ ID NO: 7) PTCHD1-x1Bf GCGCCCGCTCTGCTCTA (SEQ ID NO: 8) PTCHD1-x1Br TCCTTGTCCAGGAGGCTGGGA (SEQ ID NO: 9) PTCHD1-x2-F GAATGTCCACCCTCTCCAAA (SEQ ID NO: 10) PTCHD1-x2-R AAGGCTACTCCTGGCCTTTT (SEQ ID NO: 11) PTCHD1-x3a-F CTTTGACCCAGTAGTCCCTCA (SEQ ID NO: 12) PTCHD1-x3a-R GCACAAACCCCTTGGTGTA (SEQ ID NO: 13) PTCHD1-x3b-F TGTGATTGGGTTTTACATATATGAGTC (SEQ ID NO: 14) PTCHD1-x3b-R AGGTCAGATTTGAAGGCACAG (SEQ ID NO: 15) PTCHD1-x3c-F AAAAATGCCCTGGAAGTGC (SEQ ID NO: 16) PTCHD1-x3c-R TGTGTGAATTCTCATAACAACTCCT

The mutation screening revealed an I173V mutation.

EXAMPLE 3 Identification of Additional Markers of ASD

By sequencing the entire coding region of PTCHD1 in 900 unrelated ASD cases, six missense mutations were identified in six unrelated ASD probands (Table 7, FIG. 8). For clinical details see Table 8.

TABLE 7 XCI Status of No. of Cont Sex of Family Carrier Population Frequency Chromosomes Subject ID Exon Mutation Nucleotide Proband Transmission Type Mother Ancestry in ASD Test Family 1 1 167-kb deletion, disrupts M Mother Multiplex Skewed European 1 in 427 2067 PTCHD1 gene at Xp22.11 (M = 769 F = 1298) Family 1 1 167-kb deletion, disrupts M Mother Multiplex Skewed European 1 in 427 2067 PTCHD1 gene at Xp22.11 (M = 769 F = 1298) Family 2 2 I173V 517A > G M Mother Multiplex Random European\ 2 in 900  659 Mixed (M = 219 F = 220) Family 3 2 I173V 517A > G M Mother Simplex Random European 2 in 900  659 (M = 219 F = 220) Family 4 2 V195I 583G > A M Mother Simplex NC European 1 in 900  659 (M = 219 F = 220) Family 5 2 ML336-7II 1008-9GC > TA M Mother Simplex Random Asian 1 in 900  751* (M = 249 F = 251) Family 6 3 E479G 1436A > G M Mother Multiplex Random European 1 in 900  427 (M = 137 F = 145) Family 7 1 L73F 217C > T M Mother Multiplex NC Not 1 in 900  427 Available (M = 137 F = 145) *Out of 751 control chromosomes tested, N = 92 were Asian

TABLE 8 Subject ID Sex Mutations Clinical Details Family History Comments Family 1 M 167-kb Meet ADI and ADOS-1 criteria for diagnosis of autism. Difficulty Maternal history of Severe colic del with conversations, echoed words, repetitive interests, delay in social learning problem and during use of language. Attention Deficit and Hyperactivity Disorder articulation difficulties. early childhood (ADHD). No mental retardation (MR). Paternal history of Non-Verbal IQ = 42% ile ADHD like features. Family 1 M 167-kb Meet ADI and ADOS-1 criteria for diagnosis of autism. Difficulty Maternal history of Severe colic del with conversations, echoed words, repetitive interests, delay in social learning problem and during use of language. Attention Deficit and Hyperactivity Disorder articulation difficulties. early childhood (ADHD). No mental retardation (MR). Paternal history of Non-Verbal IQ = 23% ile ADHD like features. Family 2 M I173V Meet ADI and ADOS-1 criteria for diagnosis of autism. Highly Father had type II repetitive language and behaviour, motor mannerisms, extremely diabetes hyperactive, poor motor coordination and mental retardation, Lang: receptive = 40, <1% ile, expressive = 40, <1% ile Family 3 M I173V Meet ADI and ADOS-1 criteria for diagnosis of autism. Meet ADI No family history of and ADOS-1 criteria for diagnosis of autism. ADI social score = 25, PDD ADI communication score = 21, ADI Restricted, Repetitive, and Stereotyped Behavior Score = 11, ADI development score = 3, Normal IQ, M V1951 Diagnosed with autism at the age of 3 years and 4 months. Meet ADI No family history of FRX and head and ADOS-1 criteria for diagnosis of autism. Severe expressive and PDD CT scan was receptive language delay. No dysmorphology observed. normal Family 5 M ML336- Meet ADI and ADOS-1 criteria for diagnosis of autism. ADI social Father died of leukemia Minor 7II score = 26, ADI communication score = 14, ADI stereotype score = 5 thalassemia ADI development score: 4, ADOS social + communication score = 20, ADOS Restricted, Repetitive, and Stereotyped Behavior Score = 3, Some traits were observed that could be related to schizophrenia. Family 6 M E479G Diagnosed with high functioning autism. No family history of PDD Family 7 M L73F Meet ADI and ADOS-1 criteria for diagnosis of autism

All these mutations resulted in the substitution of highly conserved amino acids, and were inherited from unaffected carrier mothers. Based on in silico protein modeling, three mutations (L73F, I173V, V195I) are present in a predicted amino acid loop that sits outside of the cell membrane. This loop is posited to interact with the ligand, Hh. Another mutation, the 2-amino acid substitution ML336-337II was present within a predicted transmembrane domain. Finally, the E479G mutation was present within a predicted cytoplasmic amino acid loop. In five out of six families, these mutations segregated with the phenotype. Controls (439) were tested for the I173V and V195I mutations, 500 controls for ML336-337II, and 282 controls for L73F and E479G. None of these mutations were present in controls. Furthermore, the fact that these mutations were all maternally inherited to male probands, and were not observed in our control populations, indicates that the mutations are associated with ASD. In turn, it is reasonable to assume that these mutations contribute to the etiology of autism, and perhaps in-combination with other disease-related loci, give rise to the ASD phenotype.

Interestingly, in two of the ASD families reported in Tables 7/8 (Family-2 & Family-4), other ASD-related CNVs were identified. In family 2, in addition to I173V mutation, a de novo ˜1.0 Mb loss at 1p21.3 resulting in deletion of the entire DPYD gene (NM_000110.3) was identified. DPYD encodes a rate-limiting enzyme, dihydropyrimidine dehydrogenase (DPD), involved in pyrimidine metabolism. Complete DPD deficiency results in highly variable clinical outcomes, with convulsive disorders, motor retardation, and mental retardation being the most frequent manifestations. In Family-4, in addition to the V195I mutation, a 66 Kb de novo loss at 7q36.2 was identified resulting in deletion of DPP6 exon 3, and 33 amino acids towards the N-terminal end of the DPP6 protein. These cases evidence digenic involvement in ASD.

The ability of these PTCHD1-mutants to repress Gli2 expression was compared with wild type to determine if there was loss of function in the mutants. NIH10T1/2 fibroblasts were transfected with CMV-empty vector, a Gli-responsive promoter fused to the Luciferase gene (Gli2 pro), β-Gal (normalization) and PTCHD1 mutant expression plasmids. A mild loss of function of at least the E479G and ML336-7II mutants resulted in increased expression of Gli2 compared to wild type. 

1. A method of detecting a sequence variation of a PTCHD1 gene in an individual suspected of having Autism Spectrum Disorder (ASD), the method comprising: (a) amplifying a PTCHD1 nucleic acid in a biological sample comprising a PTCHD1 nucleic acid obtained from a human; (b) sequencing the PTCHD1 nucleic acid from the biological sample; and (c) detecting the presence of a sequence variant of PTCHD1, wherein the sequence variant of PTCHD1 is (i) a sequence variant of PTCHD1 comprising a deletion of at least a portion of exon 1 of PTCHD1, wherein exon 1 of PTCHD1 corresponds to positions 1-359 of SEQ ID NO: 17, (ii) a sequence variant of PTCHD1 comprising a G to A mutation at position corresponding to position 591 of SEQ ID NO: 17, (iii) a sequence variant of PTCHD1 comprising a GC to TA mutation at positions corresponding to positions 1016-1017 of SEQ ID NO: 17, or (vi) a sequence variant of PTCHD1 comprising an A to G mutation at position 1444 of SEQ ID NO:
 17. 2. The method as defined in claim 1, wherein the sequence variant of PTCHD1 is a sequence variant of PTCHD1 comprising a deletion of at least a portion of exon 1 of PTCHD1, wherein exon 1 of PTCHD1 corresponds to positions 1-359 of SEQ ID NO:
 17. 3. The method of claim 1, wherein the nucleic acid obtained from a human is genomic DNA.
 4. The method of claim 1, wherein the amplification comprises amplification with a primer pair of SEQ ID NO: 3 and SEQ ID NO:
 4. 5. The method of claim 1, additionally comprising detecting a sequence variant of PTCHD1 comprising a C to T mutation at a position corresponding to position 225 of SEQ ID NO:
 17. 6. The method of claim 1, wherein the sequence variant of PTCHD1 is a sequence variant of PTCHD1 comprising a GC to TA mutation at positions corresponding to positions 1016-1017 of SEQ ID NO:
 17. 7. The method of claim 1, wherein the sequence variant of PTCHD1 is a sequence variant of PTCHD1 comprising an A to G mutation at position 1444 of SEQ ID NO:
 17. 8. The method of claim 1, additionally comprising detecting a sequence variant of PTCHD1 comprising an A to G mutation at position 525 of SEQ ID NO:
 17. 9. The method of claim 1, wherein the biological sample is a bodily fluid or secretion.
 10. The method of claim 9, wherein the bodily fluid or secretion is selected from the group consisting of blood, serum, saliva, urine, and semen.
 11. A method of detecting a sequence variation of a PTCHD1 gene in an individual suspected of having Autism spectrum Disorder (ASD), the method comprising: (a) amplifying a PTCHD1 nucleic acid in a biological sample comprising a PTCHD1 nucleic acid obtained from a human; (b) sequencing the PTCHD1 nucleic acid from the biological sample; and (c) detecting the presence of a sequence variant of PTCHD1, wherein the sequence variant of PTCHD1 is a sequence variant of PTCHD1 comprising a deletion of at least a portion of exon 1 of PTCHD1, wherein exon 1 of PTCHD1 corresponds to positions 1-359 of SEQ ID NO:
 17. 12. The method of claim 11, wherein the nucleic acid obtained from a human is genomic DNA.
 13. The method of claim 11, wherein the amplification comprises amplification with a primer pair of SEQ ID NO: 3 and SEQ ID NO:
 4. 14. The method of claim 11, wherein the biological sample is a bodily fluid or secretion.
 15. The method of claim 14, wherein the bodily fluid or secretion is selected from the group consisting of blood, serum, saliva, urine, and semen. 